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Mettenleiter TC, Markotter W, Charron DF, Adisasmito WB, Almuhairi S, Behravesh CB, Bilivogui P, Bukachi SA, Casas N, Becerra NC, Chaudhary A, Ciacci Zanella JR, Cunningham AA, Dar O, Debnath N, Dungu B, Farag E, Gao GF, Hayman DTS, Khaitsa M, Koopmans MPG, Machalaba C, Mackenzie JS, Morand S, Smolenskiy V, Zhou L. Correction: The One Health High-Level Expert Panel (OHHLEP). One Health Outlook 2024; 6:6. [PMID: 38539273 PMCID: PMC10976718 DOI: 10.1186/s42522-024-00096-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Affiliation(s)
- Thomas C Mettenleiter
- Friedrich-Loeffler-Institut, Bundesforschungsinstitut für Tiergesundheit, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald, Insel Riems, Germany.
| | - Wanda Markotter
- Center for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.
| | | | | | - Salama Almuhairi
- National Emergency Crisis and Disasters Management Authority, Abu Dhabi, United Arab Emirates
| | | | - Pépé Bilivogui
- World Health Organization, Guinea Country Office, Conakry, Guinea
| | - Salome A Bukachi
- Institute of Anthropology, Gender and African Studies, University of Nairobi, Nairobi, Kenya
| | - Natalia Casas
- National Ministry of Health, Autonomous City of Buenos Aires, Argentina
| | | | | | - Janice R Ciacci Zanella
- Brazilian Agricultural Research Corporation, Embrapa Swine and Poultry, Concórdia, Santa Catarina, Brazil
| | | | - Osman Dar
- Global Operations Division, United Kingdom Health Security Agency, London, UK
| | - Nitish Debnath
- Fleming Fund Country Grant to Bangladesh, DAI Global, Dhaka, Bangladesh
| | - Baptiste Dungu
- Faculty of Veterinary Science, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Elmoubasher Farag
- Ministry of Public Health, Health Protection & Communicable Diseases Division, Doha, Qatar
| | - George F Gao
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - David T S Hayman
- Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
| | | | | | | | - John S Mackenzie
- Faculty of Health Sciences, Curtin University, Perth, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | | | - Vyacheslav Smolenskiy
- Federal Service for Surveillance on Consumer Rights Protection and Human Well-being (Rospotrebnadzor), Moscow, Russian Federation
| | - Lei Zhou
- Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
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Noack D, van den Hout MCGN, Embregts CWE, van IJcken WFJ, Koopmans MPG, Rockx B. Species-specific responses during Seoul orthohantavirus infection in human and rat lung microvascular endothelial cells. PLoS Negl Trop Dis 2024; 18:e0012074. [PMID: 38536871 PMCID: PMC11020687 DOI: 10.1371/journal.pntd.0012074] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 04/16/2024] [Accepted: 03/15/2024] [Indexed: 04/18/2024] Open
Abstract
Seoul orthohantavirus (SEOV) is a rat-borne zoonotic virus that is transmitted via inhalation of aerosolized infectious excreta, and can cause hemorrhagic fever with renal syndrome (HFRS) in humans worldwide. In rats, SEOV predominantly exists as a persistent infection in the absence of overt clinical signs. Lack of disease in rats is attributed to downregulation of pro-inflammatory and upregulation of regulatory host responses. As lung microvascular endothelial cells (LMECs) represent a primary target of infection in both human and rats, infections in these cells provide a unique opportunity to study the central role of LMECs in the dichotomy between pathogenicity in both species. In this study, host responses to SEOV infection in primary human and rat LMECs were directly compared on a transcriptional level. As infection of rat LMECs was more efficient than human LMECs, the majority of anti-viral defense responses were observed earlier in rat LMECs. Most prominently, SEOV-induced processes in both species included responses to cytokine stimulus, negative regulation of innate immune responses, responses to type I and II interferons, regulation of pattern recognition receptor signaling and MHC-I signaling. However, over time, in the rat LMECs, responses shifted from an anti-viral state towards a more immunotolerant state displayed by a PD-L1, B2M-, JAK2-focused interaction network aiding in negative regulation of cytotoxic CD8-positive T cell activation. This suggests a novel mechanism by which species-specific orthohantavirus-induced endothelium and T cell crosstalk may play a crucial role in the development of acute disease in humans and persistence in rodents.
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Affiliation(s)
- Danny Noack
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Mirjam C. G. N. van den Hout
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Center for Biomics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Carmen W. E. Embregts
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Wilfred F. J. van IJcken
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Center for Biomics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marion P. G. Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Barry Rockx
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
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van Roode MY, Dos S Ribeiro C, Farag E, Nour M, Moustafa A, Ahmed M, Haringhuizen G, Koopmans MPG, van de Burgwal LHM. Six dilemmas for stakeholders inherently affecting data sharing during a zoonotic (re-)emerging infectious disease outbreak response. BMC Infect Dis 2024; 24:185. [PMID: 38347527 PMCID: PMC10863217 DOI: 10.1186/s12879-024-09054-0] [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: 08/15/2023] [Accepted: 01/24/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Timely access to outbreak related data, particularly in the early events of a spillover, is important to support evidence based control measures in response to outbreaks of zoonotic Emerging Infectious Diseases (EID). Yet, this is impeded by several barriers that need to be understood to promote timely sharing of data. Using the MERS epidemic as a model for a zoonotic EID outbreak, this study sought to provide an in-depth understanding of data sharing practices. METHODS Semi-structured interviews with 25 experts were conducted, along with Focus Group Discussions with 15 additional experts. A root-cause analysis was performed to examine the causal relationships between barriers. Enablers were mapped to the root-cause analysis to understand their influence on the barriers. Finally, root causes were placed in context of core dilemmas identified from the qualitative analysis. FINDINGS Eight barriers to data sharing were identified, related to collaboration, technical preparedness, regulations, and (conflict of) interests, and placed in the context of six dilemmas inherent to the multi-stakeholder collaboration required for a zoonotic outbreak response. Fourteen identified enablers showed the willingness of stakeholders to overcome or circumvent these barriers, but also indicated the inherent trial and error nature of implementing such enablers. INTERPRETATION Addressing the barriers requires solutions that must consider the complexity and interconnectedness of the root causes underlying them, and should consider the distinct scopes and interests of the different stakeholders. Insights provided by this study can be used to encourage data sharing practices for future outbreaks FUNDING: Wellcome Trust and UK Aid; EU-H2020 Societal Challenges (grant agreement no. 643476), Nederlandse Organisatie voor Wetenschappelijk Onderzoek (VI.Veni.201S.044).
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Affiliation(s)
- Martine Y van Roode
- Department of Viroscience, Erasmus University Medical Center (Erasmus MC), Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.
| | - Carolina Dos S Ribeiro
- Center for Infectious Disease Control, The Netherlands National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Vrije Universiteit Amsterdam (VU Amsterdam), Faculty of Science, Athena Institute for Research On Innovation and Communication in Health and Life Sciences, Amsterdam, The Netherlands
| | - Elmoubasher Farag
- Department of Health Protection & Communicable Diseases, Ministry of Public Health, Doha, Qatar
| | - Mohamed Nour
- Department of Health Protection & Communicable Diseases, Ministry of Public Health, Doha, Qatar
| | - Aya Moustafa
- Department of Health Protection & Communicable Diseases, Ministry of Public Health, Doha, Qatar
| | - Minahil Ahmed
- Department of Health Protection & Communicable Diseases, Ministry of Public Health, Doha, Qatar
| | - George Haringhuizen
- Center for Infectious Disease Control, The Netherlands National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center (Erasmus MC), Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
- Pandemic and Disaster Preparedness Center (PDPC), Rotterdam, The Netherlands
| | - Linda H M van de Burgwal
- Vrije Universiteit Amsterdam (VU Amsterdam), Faculty of Science, Athena Institute for Research On Innovation and Communication in Health and Life Sciences, Amsterdam, The Netherlands
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Abourashed A, de Best PA, Doornekamp L, Sikkema RS, van Gorp ECM, Timen A, Bartumeus F, Palmer JRB, Koopmans MPG. Development and validation of the MosquitoWise survey to assess perceptions towards mosquitoes and mosquito-borne viruses in Europe. Sci Rep 2024; 14:1777. [PMID: 38245571 PMCID: PMC10799950 DOI: 10.1038/s41598-024-52219-9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 01/16/2024] [Indexed: 01/22/2024] Open
Abstract
Due to climate change and the expanding geographical ranges of key mosquito species, several mosquito-borne viruses (MBVs) have recently emerged in Europe. Understanding people's perceptions and behaviours towards these viruses and the mosquitoes capable of transmitting them is crucial for implementing effective prevention measures and targeted communication campaigns. However, there is currently no appropriate validated survey for European populations to assess this. This study developed and validated a standardized survey, based on the Health Belief Model (HBM), to assess perceptions of mosquitoes and MBVs among Europe's residents. The survey was distributed online to United Kingdom (UK), Dutch and Spanish participants through panel providers. Survey validity and reliability were tested using confirmatory factor analysis (CFA) and Cronbach's alpha. The optimised survey was completed by 336 UK, 438 Dutch and 475 Spanish residents, respectively, and the HBM items passed our validity and reliability testing in all three countries. The final survey has 57 questions, including 19 validated HBM items, and questions to assess demographic characteristics, knowledge, prevention measures and behavioural determinants. Our MosquitoWise survey bridges researchers' understandings of European residents' perceptions and knowledge as a first step to improve preventive behaviour towards mosquitoes and MBVs and guide prevention and communication initiatives.
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Affiliation(s)
- Ayat Abourashed
- Viroscience, Erasmus University Medical Center, Rotterdam, 3015 GD, The Netherlands.
- Centre d'Estudis Avançats de Blanes (CEAB-CSIC), 17300, Blanes, Spain.
| | - Pauline A de Best
- Viroscience, Erasmus University Medical Center, Rotterdam, 3015 GD, The Netherlands
- National Institute for Public Health and the Environment (RIVM), Bilthoven, 3721 MA, The Netherlands
| | - Laura Doornekamp
- Viroscience, Erasmus University Medical Center, Rotterdam, 3015 GD, The Netherlands
- Department of Medical Microbiology and Infectious Diseases, University Medical Center, Rotterdam, 3015 GD, The Netherlands
| | - Reina S Sikkema
- Viroscience, Erasmus University Medical Center, Rotterdam, 3015 GD, The Netherlands
- Centre for Avian Migration, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, The Netherlands
| | - Eric C M van Gorp
- Viroscience, Erasmus University Medical Center, Rotterdam, 3015 GD, The Netherlands
| | - Aura Timen
- National Institute for Public Health and the Environment (RIVM), Bilthoven, 3721 MA, The Netherlands
- Department of Primary and Community Care, RadboudUMC, Nijmegen, 6525 GA, The Netherlands
- Athena Institute, VU University, Amsterdam, 1081 HV, The Netherlands
| | - Frederic Bartumeus
- Centre d'Estudis Avançats de Blanes (CEAB-CSIC), 17300, Blanes, Spain
- Centre de Recerca Ecològica i Aplicacions Forestals (CREAF), 08193, Cerdanyola del Vallès, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain
| | - John R B Palmer
- Department of Political and Social Sciences, Universitat Pompeu Fabra, 08005, Barcelona, Spain
| | - Marion P G Koopmans
- Viroscience, Erasmus University Medical Center, Rotterdam, 3015 GD, The Netherlands
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Lu L, Zhang F, Oude Munnink BB, Munger E, Sikkema RS, Pappa S, Tsioka K, Sinigaglia A, Dal Molin E, Shih BB, Günther A, Pohlmann A, Ziegler U, Beer M, Taylor RA, Bartumeus F, Woolhouse M, Aarestrup FM, Barzon L, Papa A, Lycett S, Koopmans MPG. West Nile virus spread in Europe: Phylogeographic pattern analysis and key drivers. PLoS Pathog 2024; 20:e1011880. [PMID: 38271294 PMCID: PMC10810478 DOI: 10.1371/journal.ppat.1011880] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 12/04/2023] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND West Nile virus (WNV) outbreaks in birds, humans, and livestock have occurred in multiple areas in Europe and have had a significant impact on animal and human health. The patterns of emergence and spread of WNV in Europe are very different from those in the US and understanding these are important for guiding preparedness activities. METHODS We mapped the evolution and spread history of WNV in Europe by incorporating viral genome sequences and epidemiological data into phylodynamic models. Spatially explicit phylogeographic models were developed to explore the possible contribution of different drivers to viral dispersal direction and velocity. A "skygrid-GLM" approach was used to identify how changes in environments would predict viral genetic diversity variations over time. FINDINGS Among the six lineages found in Europe, WNV-2a (a sub-lineage of WNV-2) has been predominant (accounting for 73% of all sequences obtained in Europe that have been shared in the public domain) and has spread to at least 14 countries. In the past two decades, WNV-2a has evolved into two major co-circulating clusters, both originating from Central Europe, but with distinct dynamic history and transmission patterns. WNV-2a spreads at a high dispersal velocity (88km/yr-215 km/yr) which is correlated to bird movements. Notably, amongst multiple drivers that could affect the spread of WNV, factors related to land use were found to strongly influence the spread of WNV. Specifically, the intensity of agricultural activities (defined by factors related to crops and livestock production, such as coverage of cropland, pasture, cultivated and managed vegetation, livestock density) were positively associated with both spread direction and velocity. In addition, WNV spread direction was associated with high coverage of wetlands and migratory bird flyways. CONCLUSION Our results suggest that-in addition to ecological conditions favouring bird- and mosquito- presence-agricultural land use may be a significant driver of WNV emergence and spread. Our study also identified significant gaps in data and the need to strengthen virological surveillance in countries of Central Europe from where WNV outbreaks are likely seeded. Enhanced monitoring for early detection of further dispersal could be targeted to areas with high agricultural activities and habitats of migratory birds.
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Affiliation(s)
- Lu Lu
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Feifei Zhang
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Bas B. Oude Munnink
- Erasmus MC, Viroscience and Pandemic and Disaster Preparedness Centre, Rotterdam, the Netherlands
| | - Emmanuelle Munger
- Erasmus MC, Viroscience and Pandemic and Disaster Preparedness Centre, Rotterdam, the Netherlands
| | - Reina S. Sikkema
- Erasmus MC, Viroscience and Pandemic and Disaster Preparedness Centre, Rotterdam, the Netherlands
| | - Styliani Pappa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Katerina Tsioka
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | | | - Barbara B. Shih
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Anne Günther
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Riems, Germany
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Riems, Germany
| | - Ute Ziegler
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Riems, Germany
| | - Rachel A. Taylor
- Department of Epidemiological Sciences, Animal and Plant Health Agency, United Kingdom
| | - Frederic Bartumeus
- Centre for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
- Centre for Research on Ecology and Forestry Applications (CREAF), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Mark Woolhouse
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Luisa Barzon
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Anna Papa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Samantha Lycett
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Marion P. G. Koopmans
- Erasmus MC, Viroscience and Pandemic and Disaster Preparedness Centre, Rotterdam, the Netherlands
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Mettenleiter TC, Markotter W, Charron DF, Adisasmito WB, Almuhairi S, Behravesh CB, Bilivogui P, Bukachi SA, Casas N, Becerra NC, Chaudhary A, Zanella JRC, Cunningham AA, Dar O, Debnath N, Dungu B, Farag E, Gao GF, Hayman DTS, Khaitsa M, Koopmans MPG, Machalaba C, Mackenzie JS, Morand S, Smolenskiy V, Zhou L. The One Health High-Level Expert Panel (OHHLEP). One Health Outlook 2023; 5:18. [PMID: 38062534 PMCID: PMC10704771 DOI: 10.1186/s42522-023-00085-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Affiliation(s)
- Thomas C Mettenleiter
- Friedrich-Loeffler-Institut, Bundesforschungsinstitut Für Tiergesundheit, Federal Research Institute for Animal Health, Südufer 10, Greifswald, 17493, Insel Riems, Germany.
| | - Wanda Markotter
- Center for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.
| | - Dominique F Charron
- Visiting Professor, One Health Institute, University of Guelph, Guelph, ON, Canada
| | | | - Salama Almuhairi
- National Emergency Crisis and Disasters Management Authority, Abu Dhabi, United Arab Emirates
| | | | - Pépé Bilivogui
- World Health Organization, Guinea Country Office, Conakry, Guinea
| | - Salome A Bukachi
- Institute of Anthropology, Gender and African Studies, University of Nairobi, Nairobi, Kenia
| | - Natalia Casas
- National Ministry of Health, Autonomous City of Buenos Aires, Argentina
| | | | | | - Janice R Ciacci Zanella
- Brazilian Agricultural Research Corporation, Embrapa Swine and Poultry, Concórdia, Santa Catarina, Brazil
| | | | - Osman Dar
- Global Operations Division, United Kingdom Health Security Agenca, London, UK
| | - Nitish Debnath
- Fleming Fund Country Grant to Bangladesh, DAI Global, Dhaka, Bangladesh
| | - Baptiste Dungu
- Faculty of Veterinary Science, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Elmoubasher Farag
- Ministry of Public Health, Health Protection & Communicable Diseases Division, Doha, Qatar
| | - George F Gao
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - David T S Hayman
- Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
| | | | | | | | - John S Mackenzie
- Faculty of Health Sciences, Curtin University, Perth, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | | | - Vyacheslav Smolenskiy
- Federal Service for Surveillance on Consumer Rights Protection and Human Well-being (Rospotrebnadzor), Moscow, Russian Federation
| | - Lei Zhou
- Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
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Recanatini C, GeurtsvanKessel CH, Pas SD, Broens EM, Maas M, van Mansfeld R, Mutsaers-van Oudheusden AJG, van Rijen M, Schippers EF, Stegeman A, Tami A, Veldkamp KE, Visser H, Voss A, Wegdam-Blans MCA, Wertheim HFL, Wever PC, Koopmans MPG, Kluytmans JAJW, Kluytmans-van den Bergh MFQ. Seroprevalence of SARS-CoV-2 antibodies among healthcare workers in Dutch hospitals after the 2020 first wave: a multicentre cross-sectional study with prospective follow-up. Antimicrob Resist Infect Control 2023; 12:137. [PMID: 38031155 PMCID: PMC10688070 DOI: 10.1186/s13756-023-01324-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: 04/22/2023] [Accepted: 10/22/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND We aimed to estimate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seroprevalence and describe its determinants and associated symptoms among unvaccinated healthcare workers (HCWs) after the first wave of the pandemic. METHODS HCWs from 13 Dutch hospitals were screened for antibodies against the spike protein of SARS-CoV-2 in June-July 2020 and after three months. Participants completed a retrospective questionnaire on determinants for occupational and community exposure to SARS-CoV-2 and symptoms suggestive of COVID-19 experienced since January 2020. The seroprevalence was calculated per baseline characteristic and symptom at baseline and after follow-up. Adjusted odds ratios (aOR) for seropositivity were determined using logistic regression. RESULTS Among 2328 HCWs, 323 (13.9%) were seropositive at enrolment, 49 of whom (15%) reported no previous symptoms suggestive of COVID-19. During follow-up, only 1% of the tested participants seroconverted. Seroprevalence was higher in younger HCWs compared to the mid-age category (aOR 1.53, 95% CI 1.07-2.18). Nurses (aOR 2.21, 95% CI 1.34-3.64) and administrative staff (aOR 1.87, 95% CI 1.02-3.43) had a higher seroprevalence than physicians. The highest seroprevalence was observed in HCWs in the emergency department (ED) (aOR 1.79, 95% CI 1.10-2.91), the lowest in HCWs in the intensive, high, or medium care units (aOR 0.47, 95% CI 0.31-0.71). Chronic respiratory disease, smoking, and having a dog were independently associated with a lower seroprevalence, while HCWs with diabetes mellitus had a higher seroprevalence. In a multivariable model containing all self-reported symptoms since January 2020, altered smell and taste, fever, general malaise/fatigue, and muscle aches were positively associated with developing antibodies, while sore throat and chills were negatively associated. CONCLUSIONS The SARS-CoV-2 seroprevalence in unvaccinated HCWs of 13 Dutch hospitals was 14% in June-July 2020 and remained stable after three months. A higher seroprevalence was observed in the ED and among nurses, administrative and young staff, and those with diabetes mellitus, while a lower seroprevalence was found in HCWs in intensive, high, or medium care, and those with self-reported lung disease, smokers, and dog owners. A history of altered smell or taste, fever, muscle aches and fatigue were independently associated with the presence of SARS-CoV-2 antibodies in unvaccinated HCWs.
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Affiliation(s)
- Claudia Recanatini
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
| | | | - Suzan D Pas
- Microvida Laboratory for Medical Microbiology, Bravis Hospital, Roosendaal, The Netherlands
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Els M Broens
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Martje Maas
- Department of Internal Medicine, Bernhoven Hospital, Uden, The Netherlands
| | - Rosa van Mansfeld
- Department of Medical Microbiology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Miranda van Rijen
- Department of Infection Control, Amphia Hospital, Breda, The Netherlands
| | - Emile F Schippers
- Department of Internal Medicine, Haga Hospital, The Hague, The Netherlands
| | - Arjan Stegeman
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Adriana Tami
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Karin Ellen Veldkamp
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hannah Visser
- Department of Internal Medicine, Beatrix Hospital, Gorinchem, The Netherlands
| | - Andreas Voss
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marjolijn C A Wegdam-Blans
- Catharina Hospital, Eindhoven, The Netherlands
- Hospital St. Jans Gasthuis, Weert, The Netherlands
- Department of Medical Microbiology, Stichting PAMM, Veldhoven, The Netherlands
| | - Heiman F L Wertheim
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Peter C Wever
- Department of Medical Microbiology and Infection Control, Jeroen Bosch Hospital, 's Hertogenbosch, The Netherlands
| | - Marion P G Koopmans
- Viroscience Department, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jan A J W Kluytmans
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Infection Control, Amphia Hospital, Breda, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marjolein F Q Kluytmans-van den Bergh
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Infection Control, Amphia Hospital, Breda, The Netherlands
- Amphia Academy Infectious Disease Foundation, Amphia Hospital, Breda, The Netherlands
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8
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Berentschot JC, Drexhage HA, Aynekulu Mersha DG, Wijkhuijs AJM, GeurtsvanKessel CH, Koopmans MPG, Voermans JJC, Hendriks RW, Nagtzaam NMA, de Bie M, Heijenbrok-Kal MH, Bek LM, Ribbers GM, van den Berg-Emons RJG, Aerts JGJV, Dik WA, Hellemons ME. Immunological profiling in long COVID: overall low grade inflammation and T-lymphocyte senescence and increased monocyte activation correlating with increasing fatigue severity. Front Immunol 2023; 14:1254899. [PMID: 37881427 PMCID: PMC10597688 DOI: 10.3389/fimmu.2023.1254899] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/14/2023] [Indexed: 10/27/2023] Open
Abstract
Background Many patients with SARS-CoV-2 infection develop long COVID with fatigue as one of the most disabling symptoms. We performed clinical and immune profiling of fatigued and non-fatigued long COVID patients and age- and sex-matched healthy controls (HCs). Methods Long COVID symptoms were assessed using patient-reported outcome measures, including the fatigue assessment scale (FAS, scores ≥22 denote fatigue), and followed up to one year after hospital discharge. We assessed inflammation-related genes in circulating monocytes, serum levels of inflammation-regulating cytokines, and leukocyte and lymphocyte subsets, including major monocyte subsets and senescent T-lymphocytes, at 3-6 months post-discharge. Results We included 37 fatigued and 36 non-fatigued long COVID patients and 42 HCs. Fatigued long COVID patients represented a more severe clinical profile than non-fatigued patients, with many concurrent symptoms (median 9 [IQR 5.0-10.0] vs 3 [1.0-5.0] symptoms, p<0.001), and signs of cognitive failure (41%) and depression (>24%). Immune abnormalities that were found in the entire group of long COVID patients were low grade inflammation (increased inflammatory gene expression in monocytes, increased serum pro-inflammatory cytokines) and signs of T-lymphocyte senescence (increased exhausted CD8+ TEMRA-lymphocytes). Immune profiles did not significantly differ between fatigued and non-fatigued long COVID groups. However, the severity of fatigue (total FAS score) significantly correlated with increases of intermediate and non-classical monocytes, upregulated gene levels of CCL2, CCL7, and SERPINB2 in monocytes, increases in serum Galectin-9, and higher CD8+ T-lymphocyte counts. Conclusion Long COVID with fatigue is associated with many concurrent and persistent symptoms lasting up to one year after hospitalization. Increased fatigue severity associated with stronger signs of monocyte activation in long COVID patients and potentially point in the direction of monocyte-endothelial interaction. These abnormalities were present against a background of immune abnormalities common to the entire group of long COVID patients.
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Affiliation(s)
- Julia C. Berentschot
- Department of Respiratory Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Hemmo A. Drexhage
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | | | | | | | - Marion P. G. Koopmans
- Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Jolanda J. C. Voermans
- Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Rudi W. Hendriks
- Department of Respiratory Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Nicole M. A. Nagtzaam
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Maaike de Bie
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Majanka H. Heijenbrok-Kal
- Department of Rehabilitation Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- Rijndam Rehabilitation, Rotterdam, Netherlands
| | - L. Martine Bek
- Department of Rehabilitation Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Gerard M. Ribbers
- Department of Rehabilitation Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- Rijndam Rehabilitation, Rotterdam, Netherlands
| | | | - Joachim G. J. V. Aerts
- Department of Respiratory Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Willem A. Dik
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Merel E. Hellemons
- Department of Respiratory Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
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9
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Worp N, Subissi L, Perkins MD, Van Kerkhove MD, Agrawal A, Chand M, van Beek J, Oude Munnink BB, Koopmans MPG. Towards the development of a SARS-CoV-2 variant risk assessment tool: expert consultation on the assessment of scientific evidence on emerging variants. Lancet Microbe 2023; 4:e830-e836. [PMID: 37640039 DOI: 10.1016/s2666-5247(23)00179-9] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/26/2023] [Accepted: 06/05/2023] [Indexed: 08/31/2023]
Abstract
A systematic approach is required for the development of an evidence-based risk assessment tool to robustly estimate the risks and implications of SARS-CoV-2 variants. We conducted a survey among experts involved in technical advisory roles for WHO to capture their assessment of the robustness of different study types that provide evidence for potential changes in transmissibility, antigenicity, virulence, treatability, and detectability of SARS-CoV-2 variants. The views of 62 experts indicated that studies could be grouped on the basis of robustness and reliability for the different risk indicators mentioned. Several study types that experts scored as providing reliable evidence and that can be performed in a timely manner were identified. Although experts from different technical areas had varying responses, there was agreement on the highest and lowest scoring study types. These findings can help to prioritise, harmonise, and optimise study designs for the further development of a systematic, evidence-based, SARS-CoV-2 variant risk assessment tool.
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Affiliation(s)
- Nathalie Worp
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | | | | | - Anurag Agrawal
- Trivedi School of Biosciences, Ashoka University, Sonipat, India
| | | | - Janko van Beek
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands.
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10
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Markotter W, Mettenleiter TC, Adisasmito WB, Almuhairi S, Barton Behravesh C, Bilivogui P, Bukachi SA, Casas N, Cediel Becerra N, Charron DF, Chaudhary A, Ciacci Zanella JR, Cunningham AA, Dar O, Debnath N, Dungu B, Farag E, Gao GF, Hayman DTS, Khaitsa M, Koopmans MPG, Machalaba C, Mackenzie JS, Morand S, Smolenskiy V, Zhou L. Prevention of zoonotic spillover: From relying on response to reducing the risk at source. PLoS Pathog 2023; 19:e1011504. [PMID: 37796834 PMCID: PMC10553309 DOI: 10.1371/journal.ppat.1011504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023] Open
Affiliation(s)
| | - Wanda Markotter
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Thomas C. Mettenleiter
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | | | - Salama Almuhairi
- National Emergency Crisis and Disasters Management Authority, Abu Dhabi, United Arab Emirates
| | | | - Pépé Bilivogui
- World Health Organization, Guinea Country Office, Conakry, Guinea
| | - Salome A. Bukachi
- Institute of Anthropology, Gender and African Studies, University of Nairobi, Nairobi, Kenya
| | - Natalia Casas
- National Ministry of Health, Autonomous City of Buenos Aires, Argentina
| | | | - Dominique F. Charron
- Visiting Professor, One Health Institute, University of Guelph, Guelph, Ontario, Canada
| | - Abhishek Chaudhary
- Department of Civil Engineering, Indian Institute of Technology (IIT), Kanpur, India
| | - Janice R. Ciacci Zanella
- Brazilian Agricultural Research Corporation (Embrapa), Embrapa Swine and Poultry, Concórdia/SC, Brazil
| | | | - Osman Dar
- Global Operations Division, United Kingdom Health Security Agency, London, United Kingdom
- Global Health Programme, Chatham House, Royal Institute of International Affairs, London, United Kingdom
| | - Nitish Debnath
- Fleming Fund Country Grant to Bangladesh, DAI Global, Dhaka, Bangladesh
| | - Baptiste Dungu
- Onderstepoort Biological Products SOC (OBP), Afrivet, B M, Pretoria, South Africa
- Faculty of Veterinary Science, University of Kinshasa, Kinshasa, DR Congo
| | - Elmoubasher Farag
- Ministry of Public Health, Health Protection & Communicable Diseases Divison, Doha, Qatar
| | - George F. Gao
- Chinese Center for Disease Control and Prevention, Beijing, P.R. China
| | - David T. S. Hayman
- Molecular Epidemiology and Public Health Laboratory, Massey University, Palmerston North, New Zealand
| | - Margaret Khaitsa
- Mississippi State University, Starkville, Mississippi, United States of America
| | | | | | | | - Serge Morand
- IRL HealthDEEP, CNRS - Kasetsart University - Mahidol University, Bangkok, Thailand
| | - Vyacheslav Smolenskiy
- Federal Service for Surveillance on Consumer Rights Protection and Human Well-being (Rospotrebnadzor), Moscow, Russian Federation
| | - Lei Zhou
- Chinese Center for Disease Control and Prevention, Beijing, P.R. China
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11
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Crits-Christoph A, Levy JI, Pekar JE, Goldstein SA, Singh R, Hensel Z, Gangavarapu K, Rogers MB, Moshiri N, Garry RF, Holmes EC, Koopmans MPG, Lemey P, Popescu S, Rambaut A, Robertson DL, Suchard MA, Wertheim JO, Rasmussen AL, Andersen KG, Worobey M, Débarre F. Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic. bioRxiv 2023:2023.09.13.557637. [PMID: 37745602 PMCID: PMC10515900 DOI: 10.1101/2023.09.13.557637] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Wholesale Seafood Market, the site with the most reported wildlife vendors in the city of Wuhan, China. Here, we analyze publicly available qPCR and sequencing data from environmental samples collected in the Huanan market in early 2020. We demonstrate that the SARS-CoV-2 genetic diversity linked to this market is consistent with market emergence, and find increased SARS-CoV-2 positivity near and within a particular wildlife stall. We identify wildlife DNA in all SARS-CoV-2 positive samples from this stall. This includes species such as civets, bamboo rats, porcupines, hedgehogs, and one species, raccoon dogs, known to be capable of SARS-CoV-2 transmission. We also detect other animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them to those from other markets. This analysis provides the genetic basis for a short list of potential intermediate hosts of SARS-CoV-2 to prioritize for retrospective serological testing and viral sampling.
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Affiliation(s)
| | - Joshua I. Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan E. Pekar
- Department of Biomedical Informatics, University of California San Diego, La Jolla, CA, USA
| | - Stephen A. Goldstein
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Reema Singh
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Zach Hensel
- ITQB NOVA, Universidade NOVA de Lisboa, Lisbon, Av. da Republica, 2780-157, Oeiras, Portugal
| | - Karthik Gangavarapu
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Matthew B. Rogers
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Niema Moshiri
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA
| | - Robert F. Garry
- Tulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, LA 70112, USA; Zalgen Labs, Frederick, MD 21703, USA; Global Virus Network (GVN), Baltimore, MD 21201, USA
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Marion P. G. Koopmans
- Department of Viroscience, and Pandemic and Disaster Preparedness Centre., Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Saskia Popescu
- University of Maryland, School of Medicine, Department of Epidemiology & Public Health, Baltimore, MD 21201, USA
| | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - David L. Robertson
- MRC-University of Glasgow Center for Virus Research, Glasgow, G61 1QH, UK
| | - Marc A. Suchard
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Joel O. Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Angela L. Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Florence Débarre
- Institut d’Écologie et des Sciences de l’Environnement (IEES-Paris, UMR 7618), CNRS, Sorbonne Université, UPEC, IRD, INRAE, Paris, France
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12
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Kasbergen LMR, Nieuwenhuijse DF, de Bruin E, Sikkema RS, Koopmans MPG. The increasing complexity of arbovirus serology: An in-depth systematic review on cross-reactivity. PLoS Negl Trop Dis 2023; 17:e0011651. [PMID: 37738270 PMCID: PMC10550177 DOI: 10.1371/journal.pntd.0011651] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 12/30/2022] [Revised: 10/04/2023] [Accepted: 09/10/2023] [Indexed: 09/24/2023] Open
Abstract
Diagnosis of arbovirus infection or exposure by antibody testing is becoming increasingly difficult due to global expansion of arboviruses, which induce antibodies that may (cross-)react in serological assays. We provide a systematic review of the current knowledge and knowledge gaps in differential arbovirus serology. The search included Medline, Embase and Web of Science databases and identified 911 publications which were reduced to 102 after exclusion of studies not providing data on possible cross-reactivity or studies that did not meet the inclusion criteria regarding confirmation of virus exposure of reference population sets. Using a scoring system to further assess quality of studies, we show that the majority of the selected papers (N = 102) provides insufficient detail to support conclusions on specificity of serological outcomes with regards to elucidating antibody cross-reactivity. Along with the lack of standardization of assays, metadata such as time of illness onset, vaccination, infection and travel history, age and specificity of serological methods were most frequently missing. Given the critical role of serology for diagnosis and surveillance of arbovirus infections, better standards for reporting, as well as the development of more (standardized) specific serological assays that allow discrimination between exposures to multiple different arboviruses, are a large global unmet need.
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Affiliation(s)
| | - David F. Nieuwenhuijse
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Erwin de Bruin
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Reina S. Sikkema
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marion P. G. Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
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13
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Herfst S, Begeman L, Spronken MI, Poen MJ, Eggink D, de Meulder D, Lexmond P, Bestebroer TM, Koopmans MPG, Kuiken T, Richard M, Fouchier RAM. A Dutch highly pathogenic H5N6 avian influenza virus showed remarkable tropism for extra-respiratory organs and caused severe disease but was not transmissible via air in the ferret model. mSphere 2023; 8:e0020023. [PMID: 37428085 PMCID: PMC10449504 DOI: 10.1128/msphere.00200-23] [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: 04/13/2023] [Accepted: 06/01/2023] [Indexed: 07/11/2023] Open
Abstract
Continued circulation of A/H5N1 influenza viruses of the A/goose/Guangdong/1/96 lineage in poultry has resulted in the diversification in multiple genetic and antigenic clades. Since 2009, clade 2.3.4.4 hemagglutinin (HA) containing viruses harboring the internal and neuraminidase (NA) genes of other avian influenza A viruses have been detected. As a result, various HA-NA combinations, such as A/H5N1, A/H5N2, A/H5N3, A/H5N5, A/H5N6, and A/H5N8 have been identified. As of January 2023, 83 humans have been infected with A/H5N6 viruses, thereby posing an apparent risk for public health. Here, as part of a risk assessment, the in vitro and in vivo characterization of A/H5N6 A/black-headed gull/Netherlands/29/2017 is described. This A/H5N6 virus was not transmitted between ferrets via the air but was of unexpectedly high pathogenicity compared to other described A/H5N6 viruses. The virus replicated and caused severe lesions not only in respiratory tissues but also in multiple extra-respiratory tissues, including brain, liver, pancreas, spleen, lymph nodes, and adrenal gland. Sequence analyses demonstrated that the well-known mammalian adaptation substitution D701N was positively selected in almost all ferrets. In the in vitro experiments, no other known viral phenotypic properties associated with mammalian adaptation or increased pathogenicity were identified. The lack of transmission via the air and the absence of mammalian adaptation markers suggest that the public health risk of this virus is low. The high pathogenicity of this virus in ferrets could not be explained by the known mammalian pathogenicity factors and should be further studied. IMPORTANCE Avian influenza A/H5 viruses can cross the species barrier and infect humans. These infections can have a fatal outcome, but fortunately these influenza A/H5 viruses do not spread between humans. However, the extensive circulation and reassortment of A/H5N6 viruses in poultry and wild birds warrant risk assessments of circulating strains. Here an in-depth characterization of the properties of an avian A/H5N6 influenza virus isolated from a black-headed gull in the Netherlands was performed in vitro and in vivo, in ferrets. The virus was not transmissible via the air but caused severe disease and spread to extra-respiratory organs. Apart from the detection in ferrets of a mutation that increased virus replication, no other mammalian adaptation phenotypes were identified. Our results suggest that the risk of this avian A/H5N6 virus for public health is low. The underlying reasons for the high pathogenicity of this virus are unexplained and should be further studied.
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Affiliation(s)
- Sander Herfst
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Lineke Begeman
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Monique I. Spronken
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marjolein J. Poen
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Dirk Eggink
- Academic Medical Center Amsterdam, Laboratory of Experimental Virology, Amsterdam, the Netherlands
| | - Dennis de Meulder
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Pascal Lexmond
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Theo M. Bestebroer
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marion P. G. Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Thijs Kuiken
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Mathilde Richard
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Ron A. M. Fouchier
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
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14
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Schmitz D, Zwagemaker F, van der Veer B, Vennema H, Laros JFJ, Koopmans MPG, De Graaf M, Kroneman A. Metagenomic Surveillance of Viral Gastroenteritis in a Public Health Setting. Microbiol Spectr 2023; 11:e0502222. [PMID: 37432120 PMCID: PMC10434279 DOI: 10.1128/spectrum.05022-22] [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: 12/08/2022] [Accepted: 06/06/2023] [Indexed: 07/12/2023] Open
Abstract
Norovirus is the primary cause of viral gastroenteritis (GE). To investigate norovirus epidemiology, there is a need for whole-genome sequencing and reference sets consisting of complete genomes. To investigate the potential of shotgun metagenomic sequencing on the Illumina platform for whole-genome sequencing, 71 reverse transcriptase quantitative PCR (RT-qPCR) norovirus positive-feces (threshold cycle [CT], <30) samples from norovirus surveillance within The Netherlands were subjected to metagenomic sequencing. Data were analyzed through an in-house next-generation sequencing (NGS) analysis workflow. Additionally, we assessed the potential of metagenomic sequencing for the surveillance of off-target viruses that are of importance for public health, e.g., sapovirus, rotavirus A, enterovirus, parechovirus, aichivirus, adenovirus, and bocaparvovirus. A total of 60 complete and 10 partial norovirus genomes were generated, representing 7 genogroup I capsid genotypes and 12 genogroup II capsid genotypes. In addition to the norovirus genomes, the metagenomic approach yielded partial or complete genomes of other viruses for 39% of samples from children and 6.7% of samples from adults, including adenovirus 41 (N = 1); aichivirus 1 (N = 1); coxsackievirus A2 (N = 2), A4 (N = 2), A5 (N = 1), and A16 (N = 1); bocaparvovirus 1 (N = 1) and 3 (N = 1); human parechovirus 1 (N = 2) and 3 (N = 1); Rotavirus A (N = 1); and a sapovirus GI.7 (N = 1). The sapovirus GI.7 was initially not detected through RT-qPCR and warranted an update of the primer and probe set. Metagenomic sequencing on the Illumina platform robustly determines complete norovirus genomes and may be used to broaden gastroenteritis surveillance by capturing off-target enteric viruses. IMPORTANCE Viral gastroenteritis results in significant morbidity and mortality in vulnerable individuals and is primarily caused by norovirus. To investigate norovirus epidemiology, there is a need for whole-genome sequencing and reference sets consisting of full genomes. Using surveillance samples sent to the Dutch National Institute for Public Health and the Environment (RIVM), we compared metagenomics against conventional techniques, such as RT-qPCR and Sanger-sequencing, with norovirus as the target pathogen. We determined that metagenomics is a robust method to generate complete norovirus genomes, in parallel to many off-target pathogenic enteric virus genomes, thereby broadening our surveillance efforts. Moreover, we detected a sapovirus that was not detected by our validated gastroenteritis RT-qPCR panel, which exemplifies the strength of metagenomics. Our study shows that metagenomics can be used for public health gastroenteritis surveillance, the generation of reference-sets for molecular epidemiology, and how it compares to current surveillance strategies.
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Affiliation(s)
- Dennis Schmitz
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
- Erasmus Medical Center, Viroscience, Rotterdam, The Netherlands
| | - Florian Zwagemaker
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
| | - Bas van der Veer
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
| | - Harry Vennema
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
| | - Jeroen F. J. Laros
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands
| | | | | | - Annelies Kroneman
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
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15
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Izquierdo-Lara RW, Heijnen L, Oude Munnink BB, Schapendonk CME, Elsinga G, Langeveld J, Post J, Prasad DK, Carrizosa C, Been F, van Beek J, Schilperoort R, Vriend R, Fanoy E, de Schepper EIT, Sikkema RS, Molenkamp R, Aarestrup FM, Medema G, Koopmans MPG, de Graaf M. Rise and fall of SARS-CoV-2 variants in Rotterdam: Comparison of wastewater and clinical surveillance. Sci Total Environ 2023; 873:162209. [PMID: 36796689 PMCID: PMC9927792 DOI: 10.1016/j.scitotenv.2023.162209] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 06/04/2023]
Abstract
Monitoring of SARS-CoV-2 in wastewater (WW) is a promising tool for epidemiological surveillance, correlating not only viral RNA levels with the infection dynamics within the population, but also to viral diversity. However, the complex mixture of viral lineages in WW samples makes tracking of specific variants or lineages circulating in the population a challenging task. We sequenced sewage samples of 9 WW-catchment areas within the city of Rotterdam, used specific signature mutations from individual SARS-CoV-2 lineages to estimate their relative abundances in WW and compared them against those observed in clinical genomic surveillance of infected individuals between September 2020 and December 2021. We showed that especially for dominant lineages, the median of the frequencies of signature mutations coincides with the occurrence of those lineages in Rotterdam's clinical genomic surveillance. This, along with digital droplet RT-PCR targeting signature mutations of specific variants of concern (VOCs), showed that several VOCs emerged, became dominant and were replaced by the next VOC in Rotterdam at different time points during the study. In addition, single nucleotide variant (SNV) analysis provided evidence that spatio-temporal clusters can also be discerned from WW samples. We were able to detect specific SNVs in sewage, including one resulting in the Q183H amino acid change in the Spike gene, that was not captured by clinical genomic surveillance. Our results highlight the potential use of WW samples for genomic surveillance, increasing the set of epidemiological tools to monitor SARS-CoV-2 diversity.
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Affiliation(s)
- Ray W Izquierdo-Lara
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Leo Heijnen
- KWR Water Research Institute, Nieuwegein, the Netherlands
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | - Goffe Elsinga
- KWR Water Research Institute, Nieuwegein, the Netherlands
| | - Jeroen Langeveld
- Partners4urbanwater, Nijmegen, the Netherlands; Delft University of Technology, Stevinweg 1, 2628 CN Delft, the Netherlands
| | - Johan Post
- Partners4urbanwater, Nijmegen, the Netherlands
| | - Divyae K Prasad
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Christian Carrizosa
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Frederic Been
- KWR Water Research Institute, Nieuwegein, the Netherlands
| | - Janko van Beek
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | - Rianne Vriend
- Regional Public Health Service Rotterdam-Rijnmond, Rotterdam, the Netherlands
| | - Ewout Fanoy
- Regional Public Health Service Rotterdam-Rijnmond, Rotterdam, the Netherlands
| | - Evelien I T de Schepper
- Department of General Practice, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Reina S Sikkema
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | - Gertjan Medema
- KWR Water Research Institute, Nieuwegein, the Netherlands; Delft University of Technology, Stevinweg 1, 2628 CN Delft, the Netherlands; Pandemic and Disaster Preparedness Centre Rotterdam and Delft, the Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands; Pandemic and Disaster Preparedness Centre Rotterdam and Delft, the Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands; Pandemic and Disaster Preparedness Centre Rotterdam and Delft, the Netherlands.
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16
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Haanappel CP, Oude Munnink BB, Sikkema RS, Voor In 't Holt AF, de Jager H, de Boever R, Koene HHHT, Boter M, Chestakova IV, van der Linden A, Molenkamp R, Osbak KK, Arcilla MS, Vos MC, Koopmans MPG, Severin JA. Combining epidemiological data and whole genome sequencing to understand SARS-CoV-2 transmission dynamics in a large tertiary care hospital during the first COVID-19 wave in The Netherlands focusing on healthcare workers. Antimicrob Resist Infect Control 2023; 12:46. [PMID: 37165456 PMCID: PMC10170429 DOI: 10.1186/s13756-023-01247-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/29/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Healthcare facilities have been challenged by the risk of SARS-CoV-2 transmission between healthcare workers (HCW) and patients. During the first wave of the COVID-19 pandemic, infections among HCW were observed, questioning infection prevention and control (IPC) measures implemented at that time. AIM This study aimed to identify nosocomial transmission routes of SARS-CoV-2 between HCW and patients in a tertiary care hospital. METHODS All SARS-CoV-2 PCR positive HCW and patients identified between 1 March and 19 May 2020, were included in the analysis. Epidemiological data were collected from patient files and HCW contact tracing interviews. Whole genome sequences of SARS-CoV-2 were generated using Nanopore sequencing (WGS). Epidemiological clusters were identified, whereafter WGS and epidemiological data were combined for re-evaluation of epidemiological clusters and identification of potential transmission clusters. HCW infections were further classified into categories based on the likelihood that the infection was acquired via nosocomial transmission. Secondary cases were defined as COVID-19 cases in our hospital, part of a transmission cluster, of which the index case was either a patient or HCW from our hospital. FINDINGS The study population consisted of 293 HCW and 245 patients. Epidemiological data revealed 36 potential epidemiological clusters, with an estimated 222 (75.7%) HCW as secondary cases. WGS results were available for 195 HCW (88.2%) and 20 patients (12.8%) who belonged to an epidemiological cluster. Re-evaluation of the epidemiological clusters, with the available WGS data identified 31 transmission clusters with 65 (29.4%) HCW as secondary cases. Transmission clusters were all part of 18 (50.0%) previously determined epidemiological clusters, demonstrating that several larger outbreaks actually consisted, of several smaller transmission clusters. A total of 21 (7.2%) HCW infections were classified as from confirmed nosocomial, of which 18 were acquired from another HCW and 3 from a patient. CONCLUSION The majority of SARS-CoV-2 infections among HCW could be attributed to community-acquired infection. Infections among HCW that could be classified as due to nosocomial transmission, were mainly caused by HCW-to-HCW transmission rather than patient-to-HCW transmission. It is important to recognize the uncertainties of cluster analyses based solely on epidemiological data.
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Affiliation(s)
- Cynthia P Haanappel
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Reina S Sikkema
- Department of Viroscience, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Anne F Voor In 't Holt
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Herbert de Jager
- Department of Occupational Health Services, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Rieneke de Boever
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Heidy H H T Koene
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Marjan Boter
- Department of Viroscience, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Irina V Chestakova
- Department of Viroscience, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Anne van der Linden
- Department of Viroscience, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Kara K Osbak
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Maris S Arcilla
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Margreet C Vos
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Juliëtte A Severin
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands.
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17
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Mols VC, Lamers MM, Leijten LME, Breugem TI, van de Bildt MWG, van den Doel PB, Lina PHC, Koopmans MPG, Haagmans BL, Kuiken T, Begeman L. Correction for Mols et al., "Intestinal Tropism of a Betacoronavirus ( Merbecovirus) in Nathusius's Pipistrelle Bat (Pipistrellus nathusii), Its Natural Host". J Virol 2023; 97:e0059623. [PMID: 37154754 DOI: 10.1128/jvi.00596-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
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18
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Mykytyn AZ, Rosu ME, Kok A, Rissmann M, van Amerongen G, Geurtsvankessel C, de Vries RD, Munnink BBO, Smith DJ, Koopmans MPG, Lamers MM, Fouchier RAM, Haagmans BL. Antigenic mapping of emerging SARS-CoV-2 omicron variants BM.1.1.1, BQ.1.1, and XBB.1. Lancet Microbe 2023; 4:e294-e295. [PMID: 36657480 PMCID: PMC9842387 DOI: 10.1016/s2666-5247(22)00384-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 01/19/2023]
Affiliation(s)
- Anna Z Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | - Miruna E Rosu
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | - Adinda Kok
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | - Melanie Rissmann
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | | | | | - Rory D de Vries
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | - Bas B Oude Munnink
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | - Derek J Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Marion P G Koopmans
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | - Mart M Lamers
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | - Ron A M Fouchier
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | - Bart L Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands.
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Kelly L, Koopmans MPG, Horigan V, Papa A, Sikkema RS, Koren LGH, Snary EL. Assessing the quality of data for drivers of disease emergence. REV SCI TECH OIE 2023; 42:90-102. [PMID: 37232315 DOI: 10.20506/rst.42.3352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Drivers are factors that have the potential to directly or indirectly influence the likelihood of infectious diseases emerging or re-emerging. It is likely that an emerging infectious disease (EID) rarely occurs as the result of only one driver; rather, a network of sub-drivers (factors that can influence a driver) are likely to provide conditions that allow a pathogen to (re-)emerge and become established. Data on sub-drivers have therefore been used by modellers to identify hotspots where EIDs may next occur, or to estimate which sub-drivers have the greatest influence on the likelihood of their occurrence. To minimise error and bias when modelling how sub-drivers interact, and thus aid in predicting the likelihood of infectious disease emergence, researchers need good-quality data to describe these sub-drivers. This study assesses the quality of the available data on sub-drivers of West Nile virus against various criteria as a case study. The data were found to be of varying quality with regard to fulfilling the criteria. The characteristic with the lowest score was completeness, i.e. where sufficient data are available to fulfil all the requirements for the model. This is an important characteristic as an incomplete data set could lead to erroneous conclusions being drawn from modelling studies. Thus, the availability of good-quality data is essential to reduce uncertainty when estimating the likelihood of where EID outbreaks may occur and identifying the points on the risk pathway where preventive measures may be taken.
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de Graaf M, Langeveld J, Post J, Carrizosa C, Franz E, Izquierdo-Lara RW, Elsinga G, Heijnen L, Been F, van Beek J, Schilperoort R, Vriend R, Fanoy E, de Schepper EIT, Koopmans MPG, Medema G. Capturing the SARS-CoV-2 infection pyramid within the municipality of Rotterdam using longitudinal sewage surveillance. Sci Total Environ 2023; 883:163599. [PMID: 37100150 PMCID: PMC10125208 DOI: 10.1016/j.scitotenv.2023.163599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/07/2023] [Accepted: 04/15/2023] [Indexed: 05/03/2023]
Abstract
Despite high vaccination rates in the Netherlands, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to circulate. Longitudinal sewage surveillance was implemented along with the notification of cases as two parts of the surveillance pyramid to validate the use of sewage for surveillance, as an early warning tool, and to measure the effect of interventions. Sewage samples were collected from nine neighborhoods between September 2020 and November 2021. Comparative analysis and modeling were performed to understand the correlation between wastewater and case trends. Using high resolution sampling, normalization of wastewater SARS-CoV-2 concentrations, and 'normalization' of reported positive tests for testing delay and intensity, the incidence of reported positive tests could be modeled based on sewage data, and trends in both surveillance systems coincided. The high collinearity implied that high levels of viral shedding around the onset of disease largely determined SARS-CoV-2 levels in wastewater, and that the observed relationship was independent of variants of concern and vaccination levels. Sewage surveillance alongside a large-scale testing effort where 58 % of a municipality was tested, indicated a five-fold difference in the number of SARS-CoV-2-positive individuals and reported cases through standard testing. Where trends in reported positive cases were biased due to testing delay and testing behavior, wastewater surveillance can objectively display SARS-CoV-2 dynamics for both small and large locations and is sensitive enough to measure small variations in the number of infected individuals within or between neighborhoods. With the transition to a post-acute phase of the pandemic, sewage surveillance can help to keep track of re-emergence, but continued validation studies are needed to assess the predictive value of sewage surveillance with new variants. Our findings and model aid in interpreting SARS-CoV-2 surveillance data for public health decision-making and show its potential as one of the pillars of future surveillance of (re)emerging viruses.
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Affiliation(s)
- Miranda de Graaf
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands; Pandemic and Disaster Preparedness Centre Rotterdam and Delft, the Netherlands.
| | - Jeroen Langeveld
- Partners4urbanwater, Nijmegen, the Netherlands; Delft University of Technology, Stevinweg 1, 2628 CN Delft, the Netherlands
| | - Johan Post
- Partners4urbanwater, Nijmegen, the Netherlands
| | - Christian Carrizosa
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands; Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Eelco Franz
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Ray W Izquierdo-Lara
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Goffe Elsinga
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Leo Heijnen
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Frederic Been
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Janko van Beek
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | - Rianne Vriend
- Regional Public Health Service Rotterdam-Rijnmond, Rotterdam, the Netherlands
| | - Ewout Fanoy
- Regional Public Health Service Rotterdam-Rijnmond, Rotterdam, the Netherlands
| | - Evelien I T de Schepper
- Department of General Practice, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands; Pandemic and Disaster Preparedness Centre Rotterdam and Delft, the Netherlands
| | - Gertjan Medema
- Pandemic and Disaster Preparedness Centre Rotterdam and Delft, the Netherlands; KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands; Delft University of Technology, Stevinweg 1, 2628 CN Delft, the Netherlands
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21
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Tan NH, Geers D, Sablerolles RSG, Rietdijk WJR, Goorhuis A, Postma DF, Visser LG, Bogers S, van Dijk LLA, Gommers L, van Leeuwen LPM, Boerma A, Nijhof SH, van Dort KA, Koopmans MPG, Dalm VASH, Lafeber M, Kootstra NA, Huckriede ALW, van Baarle D, Zaeck LM, GeurtsvanKessel CH, de Vries RD, van der Kuy PHM. Immunogenicity of bivalent omicron (BA.1) booster vaccination after different priming regimens in health-care workers in the Netherlands (SWITCH ON): results from the direct boost group of an open-label, multicentre, randomised controlled trial. Lancet Infect Dis 2023:S1473-3099(23)00140-8. [PMID: 37088096 PMCID: PMC10188122 DOI: 10.1016/s1473-3099(23)00140-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 04/25/2023]
Abstract
BACKGROUND Bivalent mRNA-based COVID-19 vaccines encoding the ancestral and omicron spike (S) protein were developed as a countermeasure against antigenically distinct SARS-CoV-2 variants. We aimed to assess the (variant-specific) immunogenicity and reactogenicity of mRNA-based bivalent omicron (BA.1) vaccines in individuals who were primed with adenovirus-based or mRNA-based vaccines encoding the ancestral spike protein. METHODS We analysed results of the direct boost group of the SWITCH ON study, an open-label, multicentre, randomised controlled trial. Health-care workers from four academic hospitals in the Netherlands aged 18-65 years who had completed a primary COVID-19 vaccination regimen and received one booster of an mRNA-based vaccine, given no later than 3 months previously, were eligible. Participants were randomly assigned (1:1) using computer software in block sizes of 16 and 24 to receive an omicron BA.1 bivalent booster straight away (direct boost group) or a bivalent omicron BA.5 booster, postponed for 90 days (postponed boost group), stratified by priming regimen. The BNT162b2 OMI BA.1 boost was given to participants younger than 45 years, and the mRNA-1273.214 boost was given to participants 45 years or older, as per Dutch guidelines. The direct boost group, whose results are presented here, were divided into four subgroups for analysis: (1) Ad26.COV2.S (Johnson & Johnson) prime and BNT162b2 OMI BA.1 (BioNTech-Pfizer) boost (Ad/P), (2) mRNA-based prime and BNT162b2 OMI BA.1 boost (mRNA/P), (3) Ad26.COV2.S prime and mRNA-1273.214 (Moderna) boost (Ad/M), and (4) mRNA-based prime and mRNA-1273.214 boost (mRNA/M). The primary outcome was fold change in S protein S1 subunit-specific IgG antibodies before and 28 days after booster vaccination. The primary outcome and safety were assessed in all participants except those who withdrew, had a SARS-CoV-2 breakthrough infection, or had a missing blood sample at day 0 or day 28. This trial is registered with ClinicalTrials.gov, NCT05471440. FINDINGS Between Sept 2 and Oct 4, 2022, 219 (50%) of 434 eligible participants were randomly assigned to the direct boost group; 187 participants were included in the primary analyses; exclusions were mainly due to SARS-CoV-2 infection between days 0 and 28. From the 187 included participants, 138 (74%) were female and 49 (26%) were male. 42 (22%) of 187 participants received Ad/P and 44 (24%) mRNA/P (those aged <45 years), and 45 (24%) had received Ad/M and 56 (30%) mRNA/M (those aged ≥45 years). S1-specific binding antibody concentrations increased 7 days after bivalent booster vaccination and remained stable over 28 days in all four subgroups (geometric mean ratio [GMR] between day 0 and day 28 was 1·15 [95% CI 1·12-1·19] for the Ad/P group, 1·17 [1·14-1·20] for the mRNA/P group, 1·20 [1·17-1·23] for the Ad/M group, and 1·16 [1·13-1·19] for the mRNA/M group). We observed no significant difference in the GMR between the Ad/P and mRNA/P groups (p=0·51). The GMR appeared to be higher in the Ad/M group than in the mRNA/M group, but was not significant (p=0·073). Most side-effects were mild to moderate in severity and resolved within 48 h in most individuals. INTERPRETATION Booster vaccination with mRNA-1273.214 or BNT162b2 OMI BA.1 in adult healthcare workers resulted in a rapid recall of humoral and cellular immune responses independent of the priming regimen. Monitoring of SARS-CoV-2 immunity at the population level, and simultaneously antigenic drift at the virus level, remains crucial to assess the necessity and timing of COVID-19 variant-specific booster vaccinations. FUNDING The Netherlands Organization for Health Research and Development (ZonMw).
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Affiliation(s)
- Ngoc H Tan
- Department of Hospital Pharmacy, Erasmus Medical Center, Rotterdam, Netherlands
| | - Daryl Geers
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | | | - Wim J R Rietdijk
- Department of Hospital Pharmacy, Erasmus Medical Center, Rotterdam, Netherlands
| | - Abraham Goorhuis
- Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Amsterdam University Medical Centers, Amsterdam, Netherlands; Infection and Immunity, Amsterdam Public Health, University of Amsterdam, Amsterdam, Netherlands
| | - Douwe F Postma
- Department of Internal Medicine and Infectious Diseases, University Medical Center Groningen, Groningen, Netherlands
| | - Leo G Visser
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Susanne Bogers
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Laura L A van Dijk
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Lennert Gommers
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | | | - Annemarie Boerma
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, Groningen, Netherlands
| | - Sander H Nijhof
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, Groningen, Netherlands
| | - Karel A van Dort
- Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | | | - Virgil A S H Dalm
- Department of Internal Medicine, Division of Allergy and Clinical Immunology and Department of Immunology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Melvin Lafeber
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, Netherlands
| | - Neeltje A Kootstra
- Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Anke L W Huckriede
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, Groningen, Netherlands
| | - Debbie van Baarle
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, Groningen, Netherlands; Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Luca M Zaeck
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | | | - Rory D de Vries
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - P Hugo M van der Kuy
- Department of Hospital Pharmacy, Erasmus Medical Center, Rotterdam, Netherlands.
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Kuiken T, Fouchier RAM, Koopmans MPG. Being ready for the next influenza pandemic? Lancet Infect Dis 2023; 23:398-399. [PMID: 36898404 DOI: 10.1016/s1473-3099(23)00117-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 03/09/2023]
Affiliation(s)
- Thijs Kuiken
- Viroscience Department, Erasmus University Medical Centre, Rotterdam 3015 GD, Netherlands
| | - Ron A M Fouchier
- Viroscience Department, Erasmus University Medical Centre, Rotterdam 3015 GD, Netherlands
| | - Marion P G Koopmans
- Viroscience Department, Erasmus University Medical Centre, Rotterdam 3015 GD, Netherlands.
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23
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Begeman L, van Riel D, Koopmans MPG, Kuiken T. The pathogenesis of zoonotic viral infections: Lessons learned by studying reservoir hosts. Front Microbiol 2023; 14:1151524. [PMID: 37056741 PMCID: PMC10086422 DOI: 10.3389/fmicb.2023.1151524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
Zoonotic viral infections that cause severe disease or even death in some people may be asymptomatic or mild in reservoir hosts. Comparison of the pathogenesis of these two host categories may potentially explain the difference in disease. However, infections in reservoir hosts are often neglected. Therefore, we compared the pathogenesis of rabies virus, macacine alphaherpesvirus, West Nile virus, Puumala orthohantavirus, monkeypox virus, Lassa mammarenavirus, H5N1 highly pathogenic avian influenza, Marburg virus, Nipah virus, Middle East respiratory syndrome, and simian/human immunodeficiency viruses in both humans and reservoir hosts. We showed that most aspects of the pathogeneses were remarkably similar. The remaining differences lead to the identification of tipping points in the pathogeneses that are important for explaining the disease outcome in severe human cases. Further elucidating these tipping points by studying zoonotic viral infections in their reservoir hosts may teach us how to reduce the severity of zoonotic viral diseases in humans.
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Affiliation(s)
- Lineke Begeman
- Viroscience, Erasmus University Medical Centre, Rotterdam, Netherlands
- *Correspondence: Lineke Begeman,
| | - Debby van Riel
- Viroscience, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Marion P. G. Koopmans
- Viroscience, Erasmus University Medical Centre, Rotterdam, Netherlands
- Pandemic and Disaster Preparedness Centre, Rotterdam, Netherlands
| | - Thijs Kuiken
- Viroscience, Erasmus University Medical Centre, Rotterdam, Netherlands
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Shamier MC, Wismans LV, van Boheemen S, Oude Munnink BB, Koopmans MPG, van Eijck CHJ, van der Eijk AA. Looking back on the COVID-19 pandemic in an elite sports team using whole genome sequencing. J Sci Med Sport 2023:S1440-2440(23)00066-X. [PMID: 37061395 PMCID: PMC10035795 DOI: 10.1016/j.jsams.2023.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 03/25/2023]
Abstract
Objectives The aim of this study was to investigate the effectiveness of infection control measures to prevent transmission of SARS-CoV-2 within a professional sports team using whole genome sequencing (WGS). Design Prospective cohort study. Methods 74 players and staff members of a Dutch professional male football team were followed from August 2020 until May 2021. A set of health and safety measures were introduced and all participants underwent regular SARS-CoV-2 RNA testing. All positive samples were subsequently sequenced (Nanopore sequencing) to assess whether infections were acquired within the training center or in the community. Results Throughout the study period, 13 participants tested positive for SARS-CoV-2. The phylogenetic analysis revealed 3 clusters (of 2 and 3 cases respectively), indicating that 3/13 cases (23%) acquired infection from another player or staff member. The first cluster was diagnosed upon enrolment, thus transmission had occurred prior to the implementation of health and safety protocols. Finally, 4 cases were diagnosed prior to symptom onset, emphasizing that frequent testing leads to early detection and isolation. Conclusion These data show that a combination of regular testing and basic control measures can prevent outbreaks of COVID-19 in a professional sports team. WGS is an important tool to distinguish between infections introduced from the community and infections transmitted between athletes.
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Affiliation(s)
- Marc C Shamier
- Department of Viroscience, Erasmus University Medical Center, the Netherlands.
| | - Leonoor V Wismans
- Department of Surgery, Erasmus University Medical Center, the Netherlands
| | - Sander van Boheemen
- Department of Viroscience, Erasmus University Medical Center, the Netherlands
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus University Medical Center, the Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, the Netherlands
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25
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Langeveld J, Schilperoort R, Heijnen L, Elsinga G, Schapendonk CEM, Fanoy E, de Schepper EIT, Koopmans MPG, de Graaf M, Medema G. Normalisation of SARS-CoV-2 concentrations in wastewater: The use of flow, electrical conductivity and crAssphage. Sci Total Environ 2023; 865:161196. [PMID: 36581271 PMCID: PMC9791714 DOI: 10.1016/j.scitotenv.2022.161196] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 05/12/2023]
Abstract
Over the course of the Corona Virus Disease-19 (COVID-19) pandemic in 2020-2022, monitoring of the severe acute respiratory syndrome coronavirus 2 ribonucleic acid (SARS-CoV-2 RNA) in wastewater has rapidly evolved into a supplementary surveillance instrument for public health. Short term trends (2 weeks) are used as a basis for policy and decision making on measures for dealing with the pandemic. Normalisation is required to account for the dilution rate of the domestic wastewater that can strongly vary due to time- and location-dependent sewer inflow of runoff, industrial discharges and extraneous waters. The standard approach in sewage surveillance is normalisation using flow measurements, although flow based normalisation is not effective in case the wastewater volume sampled does not match the wastewater volume produced. In this paper, two alternative normalisation methods, using electrical conductivity and crAssphage have been studied and compared with the standard approach using flow measurements. For this, a total of 1116 24-h flow-proportional samples have been collected between September 2020 and August 2021 at nine monitoring locations. In addition, 221 stool samples have been analysed to determine the daily crAssphage load per person. Results show that, although crAssphage shedding rates per person vary greatly, on a population-level crAssphage loads per person per day were constant over time and similar for all catchments. Consequently, crAssphage can be used as a quantitative biomarker for populations above 5595 persons. Electrical conductivity is particularly suitable to determine dilution rates relative to dry weather flow concentrations. The overall conclusion is that flow normalisation is necessary to reliably determine short-term trends in virus circulation, and can be enhanced using crAssphage and/or electrical conductivity measurement as a quality check.
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Affiliation(s)
- Jeroen Langeveld
- Sanitary Engineering, Delft University of Technology, Stevinweg 1, 2628CN Delft, the Netherlands; Partners4UrbanWater, Graafseweg 274, 6532 ZV Nijmegen, the Netherlands.
| | - Remy Schilperoort
- Partners4UrbanWater, Graafseweg 274, 6532 ZV Nijmegen, the Netherlands
| | - Leo Heijnen
- KWR Water Research Institute, Groningenhaven 7, 3433PE Nieuwegein, the Netherlands
| | - Goffe Elsinga
- KWR Water Research Institute, Groningenhaven 7, 3433PE Nieuwegein, the Netherlands
| | - Claudia E M Schapendonk
- Department of Viroscience, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Ewout Fanoy
- GGD Department public health, municipality Rotterdam, Schiedamsedijk 95, 3000 LP Rotterdam, the Netherlands
| | - Evelien I T de Schepper
- Department of General Practice, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Gertjan Medema
- Sanitary Engineering, Delft University of Technology, Stevinweg 1, 2628CN Delft, the Netherlands; KWR Water Research Institute, Groningenhaven 7, 3433PE Nieuwegein, the Netherlands; Natural resources, Michigan State University, 1405 S Harrison Rd, East-Lansing 48823, MI, USA
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26
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Mumtaz N, Dudakovic A, Nair A, Koedam M, van Leeuwen JPTM, Koopmans MPG, Rockx B, van Wijnen AJ, van der Eerden BCJ. Zika virus alters osteogenic lineage progression of human mesenchymal stromal cells. J Cell Physiol 2023; 238:379-392. [PMID: 36538650 DOI: 10.1002/jcp.30933] [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: 02/03/2022] [Revised: 11/09/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022]
Abstract
Arboviruses target bone forming osteoblasts and perturb bone remodeling via paracrine factors. We previously reported that Zika virus (ZIKV) infection of early-stage human mesenchymal stromal cells (MSCs) inhibited the osteogenic lineage commitment of MSCs. To understand the physiological interplay between bone development and ZIKV pathogenesis, we employed a primary in vitro model to examine the biological responses of MSCs to ZIKV infection at different stages of osteogenesis. Precommitted MSCs were infected at the late stage of osteogenic stimulation (Day 7) with ZIKV (multiplicity of infection of 5). We observe that MSCs infected at the late stage of differentiation are highly susceptible to ZIKV infection similar to previous observations with early stage infected MSCs (Day 0). However, in contrast to ZIKV infection at the early stage of differentiation, infection at a later stage significantly elevates the key osteogenic markers and calcium content. Comparative RNA sequencing (RNA-seq) of early and late stage infected MSCs reveals that ZIKV infection alters the mRNA transcriptome during osteogenic induction of MSCs (1251 genes). ZIKV infection provokes a robust antiviral response at both stages of osteogenic differentiation as reflected by the upregulation of interferon responsive genes (n > 140). ZIKV infection enhances the expression of immune-related genes in early stage MSCs while increasing cell cycle genes in late stage MSCs. Remarkably, ZIKA infection in early stage MSCs also activates lipid metabolism-related pathways. In conclusion, ZIKV infection has differentiation stage-dependent effects on MSCs and this mechanistic understanding may permit the development of new therapeutic or preventative measures for bone-related effects of ZIKV infection.
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Affiliation(s)
- Noreen Mumtaz
- Department of Viroscience, Erasmus MC, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Amel Dudakovic
- Departments of Orthopedic Surgery and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Asha Nair
- Departments of Orthopedic Surgery and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Marijke Koedam
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Johannes P T M van Leeuwen
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus MC, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Barry Rockx
- Department of Viroscience, Erasmus MC, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Andre J van Wijnen
- Department of Biochemistry, University of Vermont College of Medicine, Burlington, Vermont, USA
| | - Bram C J van der Eerden
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Centre, Rotterdam, The Netherlands
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27
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Sikkema RS, de Bruin E, Ramakers C, Bentvelsen R, Li W, Bosch BJ, Westerhuis B, Haagmans B, Koopmans MPG, Fraaij PLA. Reduced Seasonal Coronavirus Antibody Responses in Children Following COVID-19 Mitigation Measures, The Netherlands. Viruses 2023; 15:212. [PMID: 36680252 PMCID: PMC9862716 DOI: 10.3390/v15010212] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 01/13/2023] Open
Abstract
SARS-CoV-2 prevention and control measures did not only impact SARS-CoV-2 circulation, but also the timing and prevalence of other seasonal respiratory viruses. Especially in children, information on exposure and infections to seasonal coronaviruses as well as SARS-CoV-2 in the first year of the pandemic is largely lacking. Therefore, we set up a one-year serological survey in a large tertiary hospital in the Netherlands. We show that seasonal coronavirus seroprevalence significantly decreased in 2021 in children less than one year, most likely due to COVID-19 control measures. The SARS-CoV-2 seroprevalence in children and adolescents increased from 0.4% to 11.3%, the highest in adolescents. This implies higher exposure rates in adolescents as compared to the general population (>18 years old). It is clear that there have been significant changes in the circulation and subsequent immunity against most respiratory pathogens as a result of the mitigation measures. The implications on shorter as well as longer term are still largely unknown, but the impact of the SARS-CoV-2 pandemic and subsequent control measures will continue to affect the dynamics of other pathogens.
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Affiliation(s)
| | - Erwin de Bruin
- Viroscience, Erasmus MC, 3015 Rotterdam, The Netherlands
| | | | - Robbert Bentvelsen
- Microvida Laboratory for Microbiology, Amphia Hospital, 4818 Breda, The Netherlands
- Department of Medical Microbiology, Leiden University Medical Center, 2333 Leiden, The Netherlands
| | - Wentao Li
- Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 Utrecht, The Netherlands
| | - Berend-Jan Bosch
- Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 Utrecht, The Netherlands
| | | | - Bart Haagmans
- Viroscience, Erasmus MC, 3015 Rotterdam, The Netherlands
| | | | - Pieter L. A. Fraaij
- Viroscience, Erasmus MC, 3015 Rotterdam, The Netherlands
- Pediatrics, Erasmus MC-Sophia Children’s Hospital, 3015 Rotterdam, The Netherlands
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28
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Zaeck LM, Lamers MM, Verstrepen BE, Bestebroer TM, van Royen ME, Götz H, Shamier MC, van Leeuwen LPM, Schmitz KS, Alblas K, van Efferen S, Bogers S, Scherbeijn S, Rimmelzwaan GF, van Gorp ECM, Koopmans MPG, Haagmans BL, GeurtsvanKessel CH, de Vries RD. Low levels of monkeypox virus-neutralizing antibodies after MVA-BN vaccination in healthy individuals. Nat Med 2023; 29:270-278. [PMID: 36257333 PMCID: PMC9873555 DOI: 10.1038/s41591-022-02090-w] [Citation(s) in RCA: 81] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/13/2022] [Indexed: 02/01/2023]
Abstract
In July 2022, the ongoing monkeypox (MPX) outbreak was declared a public health emergency of international concern. Modified vaccinia Ankara-Bavarian Nordic (MVA-BN, also known as Imvamune, JYNNEOS or Imvanex) is a third-generation smallpox vaccine that is authorized and in use as a vaccine against MPX. To date, there are no data showing MPX virus (MPXV)-neutralizing antibodies in vaccinated individuals nor vaccine efficacy against MPX. Here we show that MPXV-neutralizing antibodies can be detected after MPXV infection and after historic smallpox vaccination. However, a two-shot MVA-BN immunization series in non-primed individuals yields relatively low levels of MPXV-neutralizing antibodies. Dose-sparing of an MVA-based influenza vaccine leads to lower MPXV-neutralizing antibody levels, whereas a third vaccination with the same MVA-based vaccine significantly boosts the antibody response. As the role of MPXV-neutralizing antibodies as a correlate of protection against disease and transmissibility is currently unclear, we conclude that cohort studies following vaccinated individuals are necessary to assess vaccine efficacy in at-risk populations.
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Affiliation(s)
- Luca M. Zaeck
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Mart M. Lamers
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Babs E. Verstrepen
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Theo M. Bestebroer
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Martin E. van Royen
- grid.5645.2000000040459992XDepartment of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Hannelore Götz
- grid.491204.a0000 0004 0459 9540Department Infectious Disease Control, Municipal Public Health Service Rotterdam–Rijnmond (GGD Rotterdam), Rotterdam, Netherlands
| | - Marc C. Shamier
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Leanne P. M. van Leeuwen
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Katharina S. Schmitz
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Kimberley Alblas
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Suzanne van Efferen
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Susanne Bogers
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Sandra Scherbeijn
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Guus F. Rimmelzwaan
- grid.412970.90000 0001 0126 6191Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Eric C. M. van Gorp
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Marion P. G. Koopmans
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Bart L. Haagmans
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Corine H. GeurtsvanKessel
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Rory D. de Vries
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
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29
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Jonker L, Linde KJ, de Hoog MLA, Sprado R, Huisman RC, Molenkamp R, Oude Munnink BB, Dohmen W, Heederik DJJ, Eggink D, Welkers MRA, Vennema H, Fraaij PLA, Koopmans MPG, Wouters IM, Bruijning-Verhagen PCJL. SARS-CoV-2 outbreaks in secondary school settings in the Netherlands during fall 2020; silent circulation. BMC Infect Dis 2022; 22:960. [PMID: 36572861 PMCID: PMC9791966 DOI: 10.1186/s12879-022-07904-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 11/29/2022] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND In fall 2020 when schools in the Netherlands operated under a limited set of COVID-19 measures, we conducted outbreaks studies in four secondary schools to gain insight in the level of school transmission and the role of SARS-CoV-2 transmission via air and surfaces. METHODS Outbreak studies were performed between 11 November and 15 December 2020 when the wild-type variant of SARS-CoV-2 was dominant. Clusters of SARS-CoV-2 infections within schools were identified through a prospective school surveillance study. All school contacts of cluster cases, irrespective of symptoms, were invited for PCR testing twice within 48 h and 4-7 days later. Combined NTS and saliva samples were collected at each time point along with data on recent exposure and symptoms. Surface and active air samples were collected in the school environment. All samples were PCR-tested and sequenced when possible. RESULTS Out of 263 sampled school contacts, 24 tested SARS-CoV-2 positive (secondary attack rate 9.1%), of which 62% remained asymptomatic and 42% had a weakly positive test result. Phylogenetic analysis on 12 subjects from 2 schools indicated a cluster of 8 and 2 secondary cases, respectively, but also other distinct strains within outbreaks. Of 51 collected air and 53 surface samples, none were SARS-CoV-2 positive. CONCLUSION Our study confirmed within school SARS-CoV-2 transmission and substantial silent circulation, but also multiple introductions in some cases. Absence of air or surface contamination suggests environmental contamination is not widespread during school outbreaks.
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Affiliation(s)
- Lotte Jonker
- grid.7692.a0000000090126352Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Kimberly J. Linde
- grid.5477.10000000120346234Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands
| | - Marieke L. A. de Hoog
- grid.7692.a0000000090126352Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Robin Sprado
- grid.7692.a0000000090126352Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Robin C. Huisman
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GD Rotterdam, The Netherlands
| | - Richard Molenkamp
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GD Rotterdam, The Netherlands
| | - Bas B. Oude Munnink
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GD Rotterdam, The Netherlands
| | - Wietske Dohmen
- grid.5477.10000000120346234Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands
| | - Dick J. J. Heederik
- grid.5477.10000000120346234Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands
| | - Dirk Eggink
- grid.31147.300000 0001 2208 0118Center for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie Van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Matthijs R. A. Welkers
- grid.31147.300000 0001 2208 0118Center for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie Van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands ,grid.509540.d0000 0004 6880 3010Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - Harry Vennema
- grid.31147.300000 0001 2208 0118Center for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie Van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Pieter L. A. Fraaij
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GD Rotterdam, The Netherlands ,grid.416135.40000 0004 0649 0805Department of Pediatrics, Subdivision Infectious Diseases and Immunology, Erasmus Medical Center-Sophia Children’s Hospital, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Marion P. G. Koopmans
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GD Rotterdam, The Netherlands
| | - Inge M. Wouters
- grid.5477.10000000120346234Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands
| | - Patricia C. J. L. Bruijning-Verhagen
- grid.7692.a0000000090126352Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
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30
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Molendijk MM, Phan MVT, Bode LGM, Strepis N, Prasad DK, Worp N, Nieuwenhuijse DF, Schapendonk CME, Boekema BKHL, Verbon A, Koopmans MPG, de Graaf M, van Wamel WJB. Microcalorimetry: A Novel Application to Measure In Vitro Phage Susceptibility of Staphylococcus aureus in Human Serum. Viruses 2022; 15:14. [PMID: 36680055 PMCID: PMC9865112 DOI: 10.3390/v15010014] [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] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Infections involving antibiotic resistant Staphylococcus aureus (S. aureus) represent a major challenge to successful treatment. Further, although bacteriophages (phages) could be an alternative to antibiotics, there exists a lack of correlation in phage susceptibility results between conventional in vitro and in vivo assays. This discrepancy may hinder the potential implementation of bacteriophage therapy. In this study, the susceptibility of twelve S. aureus strains to three commercial phage cocktails and two single phages was assessed. These S. aureus strains (including ten clinical isolates, five of which were methicillin-resistant) were compared using four assays: the spot test, efficiency of plating (EOP), the optical density assay (all in culture media) and microcalorimetry in human serum. In the spot test, EOP and optical density assay, all cocktails and single phages lysed both methicillin susceptible and methicillin resistant S. aureus strains. However, there was an absence of phage-mediated lysis in high concentrations of human serum as measured using microcalorimetry. As this microcalorimetry-based assay more closely resembles in vivo conditions, we propose that microcalorimetry could be included as a useful addition to conventional assays, thereby facilitating more accurate predictions of the in vivo susceptibility of S. aureus to phages during phage selection for therapeutic purposes.
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Affiliation(s)
- Michèle M. Molendijk
- Department Medical Microbiology and Infectious Diseases, Erasmus MC, 3015 Rotterdam, The Netherlands
- Department of Viroscience, Erasmus MC, 3015 Rotterdam, The Netherlands
| | - My V. T. Phan
- Department of Viroscience, Erasmus MC, 3015 Rotterdam, The Netherlands
- Medical Research Council/Uganda Virus Research Institute, London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe P.O. Box 49, Uganda
| | - Lonneke G. M. Bode
- Department Medical Microbiology and Infectious Diseases, Erasmus MC, 3015 Rotterdam, The Netherlands
| | - Nikolas Strepis
- Department Medical Microbiology and Infectious Diseases, Erasmus MC, 3015 Rotterdam, The Netherlands
| | - Divyae K. Prasad
- Department of Viroscience, Erasmus MC, 3015 Rotterdam, The Netherlands
| | - Nathalie Worp
- Department of Viroscience, Erasmus MC, 3015 Rotterdam, The Netherlands
| | | | | | | | - Annelies Verbon
- Department Medical Microbiology and Infectious Diseases, Erasmus MC, 3015 Rotterdam, The Netherlands
| | | | - Miranda de Graaf
- Department of Viroscience, Erasmus MC, 3015 Rotterdam, The Netherlands
| | - Willem J. B. van Wamel
- Department Medical Microbiology and Infectious Diseases, Erasmus MC, 3015 Rotterdam, The Netherlands
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31
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Mumtaz N, Koedam M, van Leeuwen JPTM, Koopmans MPG, van der Eerden BCJ, Rockx B. Zika virus infects human osteoclasts and blocks differentiation and bone resorption. Emerg Microbes Infect 2022; 11:1621-1634. [PMID: 35670284 PMCID: PMC9225750 DOI: 10.1080/22221751.2022.2086069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Bone-related complications are commonly reported following arbovirus infection. These arboviruses are known to disturb bone-remodeling and induce inflammatory bone loss via increased activity of bone resorbing osteoclasts (OCs). We previously showed that Zika virus (ZIKV) could disturb the function of bone forming osteoblasts, but the susceptibility of OCs to ZIKV infection is not known. Here, we investigated the effect of ZIKV infection on osteoclastogenesis and report that infection of pre- and early OCs with ZIKV significantly reduced the osteoclast formation and bone resorption. Interestingly, infection of pre-OCs with a low dose ZIKV infection in the presence of flavivirus cross-reacting antibodies recapitulated the phenotype observed with a high viral dose, suggesting a role for antibody-dependent enhancement in ZIKV-associated bone pathology. In conclusion, we have characterized a primary in vitro model to study the role of osteoclastogenesis in ZIKV pathogenesis, which will help to identify possible new targets for developing therapeutic and preventive measures.
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Affiliation(s)
- Noreen Mumtaz
- Department of Viroscience, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Marijke Koedam
- Department of Internal Medicine, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | | | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Bram C J van der Eerden
- Department of Internal Medicine, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Barry Rockx
- Department of Viroscience, Erasmus University Medical Centre, Rotterdam, the Netherlands
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32
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Tan NH, Sablerolles RSG, Rietdijk WJR, Goorhuis A, Postma DF, Visser LG, Bogers S, Geers D, Zaeck LM, Koopmans MPG, Dalm VASH, Kootstra NA, Huckriede ALW, van Baarle D, Lafeber M, GeurtsvanKessel CH, de Vries RD, van der Kuy PHM. Analyzing the immunogenicity of bivalent booster vaccinations in healthcare workers: The SWITCH ON trial protocol. Front Immunol 2022; 13:1067749. [PMID: 36524126 PMCID: PMC9744953 DOI: 10.3389/fimmu.2022.1067749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/15/2022] [Indexed: 11/30/2022] Open
Abstract
Vaccination against coronavirus disease 2019 (COVID-19) has contributed greatly to providing protection against severe disease, thereby reducing hospital admissions and deaths. Several studies have reported reduction in vaccine effectiveness over time against the Omicron sub-lineages. However, the willingness to receive regular booster doses in the general population is declining. To determine the need for repeated booster vaccinations in healthy individuals and to aid policymakers in future public health interventions for COVID-19, we aim to gain insight into the immunogenicity of the additional bivalent booster vaccination in a representative sample of the healthy Dutch population. The SWITCH ON study was initiated to investigate three main topics: i) immunogenicity of bivalent vaccines after priming with adenovirus- or mRNA-based vaccines, ii) immunological recall responses and reactivity with relevant variants after booster vaccination, and iii) the necessity of booster vaccinations for the healthy population in the future. Clinical trial registration https://clinicaltrials.gov/, identifier NCT05471440.
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Affiliation(s)
- Ngoc H. Tan
- Department of Hospital Pharmacy, Erasmus Medical Center, Rotterdam, Netherlands
| | | | - Wim J. R. Rietdijk
- Department of Hospital Pharmacy, Erasmus Medical Center, Rotterdam, Netherlands
| | - Abraham Goorhuis
- Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Amsterdam University Medical Centers, Amsterdam, Netherlands,Infection & Immunity, Amsterdam Public Health, University of Amsterdam, Amsterdam, Netherlands
| | - Douwe F. Postma
- Department of Internal Medicine and Infectious Diseases, University Medical Center Groningen, Groningen, Netherlands
| | - Leo G. Visser
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Susanne Bogers
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Daryl Geers
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Luca M. Zaeck
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | | | - Virgil A. S. H. Dalm
- Department of Internal Medicine, Division of Allergy & Clinical Immunology and Department of Immunology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Neeltje A. Kootstra
- Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Infection and Immunity Institute, University of Amsterdam, Amsterdam, Netherlands
| | - Anke L. W. Huckriede
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Debbie van Baarle
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands,Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Melvin Lafeber
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, Netherlands
| | | | - Rory D. de Vries
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Paul-Hugo Marie van der Kuy
- Department of Hospital Pharmacy, Erasmus Medical Center, Rotterdam, Netherlands,*Correspondence: Paul-Hugo Marie van der Kuy,
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33
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Embregts CWE, Farag EABA, Bansal D, Boter M, van der Linden A, Vaes VP, van Middelkoop-van den Berg I, IJpelaar J, Ziglam H, Coyle PV, Ibrahim I, Mohran KA, Alrajhi MMS, Islam MM, Abdeen R, Al-Zeyara AA, Younis NM, Al-Romaihi HE, AlThani MHJ, Sikkema RS, Koopmans MPG, Oude Munnink BB, GeurtsvanKessel CH. Rabies Virus Populations in Humans and Mice Show Minor Inter-Host Variability within Various Central Nervous System Regions and Peripheral Tissues. Viruses 2022; 14:v14122661. [PMID: 36560665 PMCID: PMC9781572 DOI: 10.3390/v14122661] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/20/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022] Open
Abstract
Rabies virus (RABV) has a broad host range and infects multiple cell types throughout the infection cycle. Next-generation sequencing (NGS) and minor variant analysis are powerful tools for studying virus populations within specific hosts and tissues, leading to novel insights into the mechanisms of host-switching and key factors for infecting specific cell types. In this study we investigated RABV populations and minor variants in both original (non-passaged) samples and in vitro-passaged isolates of various CNS regions (hippocampus, medulla oblongata and spinal cord) of a fatal human rabies case, and of multiple CNS and non-CNS tissues of experimentally infected mice. No differences in virus populations were detected between the human CNS regions, and only one non-synonymous single nucleotide polymorphism (SNP) was detected in the fifth in vitro passage of virus isolated from the spinal cord. However, the appearance of this SNP shows the importance of sequencing newly passaged virus stocks before further use. Similarly, we did not detect apparent differences in virus populations isolated from different CNS and non-CNS tissues of experimentally infected mice. Sequencing of viruses obtained from pharyngeal swab and salivary gland proved difficult, and we propose methods for improving sampling.
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Affiliation(s)
- Carmen W. E. Embregts
- Department of Viroscience, Erasmus Medical Centre, 3015 GD Rotterdam, The Netherlands
- Correspondence:
| | | | | | - Marjan Boter
- Department of Viroscience, Erasmus Medical Centre, 3015 GD Rotterdam, The Netherlands
| | - Anne van der Linden
- Department of Viroscience, Erasmus Medical Centre, 3015 GD Rotterdam, The Netherlands
| | - Vincent P. Vaes
- Department of Viroscience, Erasmus Medical Centre, 3015 GD Rotterdam, The Netherlands
| | | | - Jeroen. IJpelaar
- Department of Viroscience, Erasmus Medical Centre, 3015 GD Rotterdam, The Netherlands
| | - Hisham Ziglam
- Hamad Medical Corporation, Doha P.O. Box 3050, Qatar
| | | | - Imad Ibrahim
- Hamad Medical Corporation, Doha P.O. Box 3050, Qatar
- Biomedical Research Centre, Qatar University, Doha P.O. Box 2713, Qatar
| | - Khaled A. Mohran
- Department of Animal Resources, Ministry of Municipality, Doha P.O. Box 35081, Qatar
- Biotechnology Departments ERC, Animal Health Research Institute, Dokki 12611, Egypt
| | | | - Md. Mazharul Islam
- Department of Animal Resources, Ministry of Municipality, Doha P.O. Box 35081, Qatar
| | - Randa Abdeen
- Department of Animal Resources, Ministry of Municipality, Doha P.O. Box 35081, Qatar
| | - Abdul Aziz Al-Zeyara
- Department of Animal Resources, Ministry of Municipality, Doha P.O. Box 35081, Qatar
| | - Nidal Mahmoud Younis
- Department of Animal Resources, Ministry of Municipality, Doha P.O. Box 35081, Qatar
| | | | | | - Reina S. Sikkema
- Department of Viroscience, Erasmus Medical Centre, 3015 GD Rotterdam, The Netherlands
| | - Marion P. G. Koopmans
- Department of Viroscience, Erasmus Medical Centre, 3015 GD Rotterdam, The Netherlands
| | - Bas B. Oude Munnink
- Department of Viroscience, Erasmus Medical Centre, 3015 GD Rotterdam, The Netherlands
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34
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Kwok KTT, de Rooij MMT, Messink AB, Wouters IM, Smit LAM, Cotten M, Heederik DJJ, Koopmans MPG, Phan MVT. Establishing farm dust as a useful viral metagenomic surveillance matrix. Sci Rep 2022; 12:16308. [PMID: 36175536 PMCID: PMC9521564 DOI: 10.1038/s41598-022-20701-x] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 09/16/2022] [Indexed: 11/26/2022] Open
Abstract
Farm animals may harbor viral pathogens, some with zoonotic potential which can possibly cause severe clinical outcomes in animals and humans. Documenting the viral content of dust may provide information on the potential sources and movement of viruses. Here, we describe a dust sequencing strategy that provides detailed viral sequence characterization from farm dust samples and use this method to document the virus communities from chicken farm dust samples and paired feces collected from the same broiler farms in the Netherlands. From the sequencing data, Parvoviridae and Picornaviridae were the most frequently found virus families, detected in 85-100% of all fecal and dust samples with a large genomic diversity identified from the Picornaviridae. Sequences from the Caliciviridae and Astroviridae familes were also obtained. This study provides a unique characterization of virus communities in farmed chickens and paired farm dust samples and our sequencing methodology enabled the recovery of viral genome sequences from farm dust, providing important tracking details for virus movement between livestock animals and their farm environment. This study serves as a proof of concept supporting dust sampling to be used in viral metagenomic surveillance.
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Affiliation(s)
- Kirsty T T Kwok
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.
| | - Myrna M T de Rooij
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Aniek B Messink
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Inge M Wouters
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Lidwien A M Smit
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Matthew Cotten
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Dick J J Heederik
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - My V T Phan
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
- London School of Hygiene and Tropical Medicine, London, UK.
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35
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Mykytyn AZ, Rissmann M, Kok A, Rosu ME, Schipper D, Breugem TI, van den Doel PB, Chandler F, Bestebroer T, de Wit M, van Royen ME, Molenkamp R, Oude Munnink BB, de Vries RD, GeurtsvanKessel C, Smith DJ, Koopmans MPG, Rockx B, Lamers MM, Fouchier R, Haagmans BL. Antigenic cartography of SARS-CoV-2 reveals that Omicron BA.1 and BA.2 are antigenically distinct. Sci Immunol 2022; 7:eabq4450. [PMID: 35737747 PMCID: PMC9273038 DOI: 10.1126/sciimmunol.abq4450] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/14/2022] [Indexed: 12/16/2022]
Abstract
The emergence and rapid spread of SARS-CoV-2 variants may affect vaccine efficacy substantially. The Omicron variant termed BA.2, which differs substantially from BA.1 based on genetic sequence, is currently replacing BA.1 in several countries, but its antigenic characteristics have not yet been assessed. Here, we used antigenic cartography to quantify and visualize antigenic differences between early SARS-CoV-2 variants (614G, Alpha, Beta, Gamma, Zeta, Delta, and Mu) using hamster antisera obtained after primary infection. We first verified that the choice of the cell line for the neutralization assay did not affect the topology of the map substantially. Antigenic maps generated using pseudo-typed SARS-CoV-2 on the widely used VeroE6 cell line and the human airway cell line Calu-3 generated similar maps. Maps made using authentic SARS-CoV-2 on Calu-3 cells also closely resembled those generated with pseudo-typed viruses. The antigenic maps revealed a central cluster of SARS-CoV-2 variants, which grouped on the basis of mutual spike mutations. Whereas these early variants are antigenically similar, clustering relatively close to each other in antigenic space, Omicron BA.1 and BA.2 have evolved as two distinct antigenic outliers. Our data show that BA.1 and BA.2 both escape vaccine-induced antibody responses as a result of different antigenic characteristics. Thus, antigenic cartography could be used to assess antigenic properties of future SARS-CoV-2 variants of concern that emerge and to decide on the composition of novel spike-based (booster) vaccines.
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Affiliation(s)
- Anna Z. Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Melanie Rissmann
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Adinda Kok
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Miruna E. Rosu
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Debby Schipper
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Tim I. Breugem
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | | | - Felicity Chandler
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Theo Bestebroer
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Maurice de Wit
- Department of Neurology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Martin E. van Royen
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Richard Molenkamp
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | | | - Rory D. de Vries
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | | | - Derek J. Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | | | - Barry Rockx
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Mart M. Lamers
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Ron Fouchier
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Bart L. Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
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36
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Linde KJ, Wouters IM, Kluytmans JAJW, Kluytmans-van den Bergh MFQ, Pas SD, GeurtsvanKessel CH, Koopmans MPG, Meier M, Meijer P, Raben CR, Spithoven J, Tersteeg-Zijderveld MHG, Heederik DJJ, Dohmen W. Detection of SARS-CoV-2 in Air and on Surfaces in Rooms of Infected Nursing Home Residents. Ann Work Expo Health 2022; 67:129-140. [PMID: 36068657 PMCID: PMC9834894 DOI: 10.1093/annweh/wxac056] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/12/2022] [Accepted: 07/29/2022] [Indexed: 01/14/2023] Open
Abstract
There is an ongoing debate on airborne transmission of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) as a risk factor for infection. In this study, the level of SARS-CoV-2 in air and on surfaces of SARS-CoV-2 infected nursing home residents was assessed to gain insight in potential transmission routes. During outbreaks, air samples were collected using three different active and one passive air sampling technique in rooms of infected patients. Oropharyngeal swabs (OPS) of the residents and dry surface swabs were collected. Additionally, longitudinal passive air samples were collected during a period of 4 months in common areas of the wards. Presence of SARS-CoV-2 RNA was determined using RT-qPCR, targeting the RdRp- and E-genes. OPS, samples of two active air samplers and surface swabs with Ct-value ≤35 were tested for the presence of infectious virus by cell culture. In total, 360 air and 319 surface samples from patient rooms and common areas were collected. In rooms of 10 residents with detected SARS-CoV-2 RNA in OPS, SARS-CoV-2 RNA was detected in 93 of 184 collected environmental samples (50.5%) (lowest Ct 29.5), substantially more than in the rooms of residents with negative OPS on the day of environmental sampling (n = 2) (3.6%). SARS-CoV-2 RNA was most frequently present in the larger particle size fractions [>4 μm 60% (6/10); 1-4 μm 50% (5/10); <1 μm 20% (2/10)] (Fischer exact test P = 0.076). The highest proportion of RNA-positive air samples on room level was found with a filtration-based sampler 80% (8/10) and the cyclone-based sampler 70% (7/10), and impingement-based sampler 50% (5/10). SARS-CoV-2 RNA was detected in 10 out of 12 (83%) passive air samples in patient rooms. Both high-touch and low-touch surfaces contained SARS-CoV-2 genome in rooms of residents with positive OPS [high 38% (21/55); low 50% (22/44)]. In one active air sample, infectious virus in vitro was detected. In conclusion, SARS-CoV-2 is frequently detected in air and on surfaces in the immediate surroundings of room-isolated COVID-19 patients, providing evidence of environmental contamination. The environmental contamination of SARS-CoV-2 and infectious aerosols confirm the potential for transmission via air up to several meters.
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Affiliation(s)
- Kimberly J Linde
- Author to whom correspondence should be addressed. Tel: +31302535358; e-mail:
| | - Inge M Wouters
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Jan A J W Kluytmans
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marjolein F Q Kluytmans-van den Bergh
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands,Department of Infection Control, Amphia Hospital, Breda, The Netherlands
| | - Suzan D Pas
- Microvida Location Amphia/Bravis, Breda/Roosendaal, The Netherlands
| | | | | | | | - Patrick Meijer
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Ceder R Raben
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Jack Spithoven
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | | | - Dick J J Heederik
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Wietske Dohmen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
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37
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Bauer L, Rissmann M, Benavides FFW, Leijten L, van Run P, Begeman L, Veldhuis Kroeze EJB, Lendemeijer B, Smeenk H, de Vrij FMS, Kushner SA, Koopmans MPG, Rockx B, van Riel D. In vitro and in vivo differences in neurovirulence between D614G, Delta And Omicron BA.1 SARS-CoV-2 variants. Acta Neuropathol Commun 2022; 10:124. [PMID: 36058935 PMCID: PMC9441226 DOI: 10.1186/s40478-022-01426-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 06/20/2022] [Accepted: 08/09/2022] [Indexed: 01/16/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is associated with various neurological complications. Although the mechanism is not fully understood, several studies have shown that neuroinflammation occurs in the acute and post-acute phase. As these studies have predominantly been performed with isolates from 2020, it is unknown if there are differences among SARS-CoV-2 variants in their ability to cause neuroinflammation. Here, we compared the neuroinvasiveness, neurotropism and neurovirulence of the SARS-CoV-2 ancestral strain D614G, the Delta (B.1.617.2) and Omicron BA.1 (B.1.1.529) variants using in vitro and in vivo models. The Omicron BA.1 variant showed reduced neurotropism and neurovirulence compared to Delta and D614G in human induced pluripotent stem cell (hiPSC)-derived cortical neurons co-cultured with astrocytes. Similar differences were obtained in Syrian hamsters inoculated with D614G, Delta and the Omicron BA.1 variant 5 days post infection. Replication in the olfactory mucosa was observed in all hamsters, but most prominently in D614G inoculated hamsters. Furthermore, neuroinvasion into the CNS via the olfactory nerve was observed in D614G, but not Delta or Omicron BA.1 inoculated hamsters. Furthermore, neuroinvasion was associated with neuroinflammation in the olfactory bulb of hamsters inoculated with D614G. Altogether, our findings suggest differences in the neuroinvasive, neurotropic and neurovirulent potential between SARS-CoV-2 variants using in vitro hiPSC-derived neural cultures and in vivo in hamsters during the acute phase of the infection.
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Affiliation(s)
- Lisa Bauer
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Melanie Rissmann
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Lonneke Leijten
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Peter van Run
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lineke Begeman
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Bas Lendemeijer
- Department of Psychiatry, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Hilde Smeenk
- Department of Psychiatry, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Femke M S de Vrij
- Department of Psychiatry, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Steven A Kushner
- Department of Psychiatry, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Barry Rockx
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Debby van Riel
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
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38
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Worobey M, Levy JI, Serrano LM, Crits-Christoph A, Pekar JE, Goldstein SA, Rasmussen AL, Kraemer MUG, Newman C, Koopmans MPG, Suchard MA, Wertheim JO, Lemey P, Robertson DL, Garry RF, Holmes EC, Rambaut A, Andersen KG. The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic. Science 2022; 377:951-959. [PMID: 35881010 PMCID: PMC9348750 DOI: 10.1126/science.abp8715] [Citation(s) in RCA: 125] [Impact Index Per Article: 62.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/18/2022] [Indexed: 12/25/2022]
Abstract
Understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 is critical to preventing future zoonotic outbreaks before they become the next pandemic. The Huanan Seafood Wholesale Market in Wuhan, China, was identified as a likely source of cases in early reports, but later this conclusion became controversial. We show here that the earliest known COVID-19 cases from December 2019, including those without reported direct links, were geographically centered on this market. We report that live SARS-CoV-2-susceptible mammals were sold at the market in late 2019 and that within the market, SARS-CoV-2-positive environmental samples were spatially associated with vendors selling live mammals. Although there is insufficient evidence to define upstream events, and exact circumstances remain obscure, our analyses indicate that the emergence of SARS-CoV-2 occurred through the live wildlife trade in China and show that the Huanan market was the epicenter of the COVID-19 pandemic.
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Affiliation(s)
- Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Joshua I. Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Lorena Malpica Serrano
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Alexander Crits-Christoph
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Jonathan E. Pekar
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093, USA
- Department of Biomedical Informatics, University of California San Diego, La Jolla, CA 92093, USA
| | - Stephen A. Goldstein
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Angela L. Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon SK S7N 5E3, Canada
- Center for Global Health Science and Security, Georgetown University, Washington, DC 20057, USA
| | | | - Chris Newman
- Wildlife Conservation Research Unit, Department of Zoology, The Recanati-Kaplan Centre, University of Oxford, Oxford OX13 5QL, UK
| | - Marion P. G. Koopmans
- Pandemic and Disaster Preparedness Centre, Erasmus University Medical Center, 3015 CE Rotterdam, Netherlands
- Department of Viroscience, Erasmus University Medical Center, 3015 CE Rotterdam, Netherlands
| | - Marc A. Suchard
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Joel O. Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
- Global Virus Network (GVN), Baltimore, MD 21201, USA
| | - David L. Robertson
- MRC-University of Glasgow Center for Virus Research, Glasgow G61 1QH, UK
| | - Robert F. Garry
- Global Virus Network (GVN), Baltimore, MD 21201, USA
- Tulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, LA 70112, USA
- Zalgen Labs, Frederick, MD 21703, USA
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
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39
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Villabruna N, Izquierdo-Lara RW, Schapendonk CME, de Bruin E, Chandler F, Thao TTN, Westerhuis BM, van Beek J, Sigfrid L, Giaquinto C, Goossens H, Bielicki JA, Kohns Vasconcelos M, Fraaij PLA, Koopmans MPG, de Graaf M. Profiling of humoral immune responses to norovirus in children across Europe. Sci Rep 2022; 12:14275. [PMID: 35995986 PMCID: PMC9395339 DOI: 10.1038/s41598-022-18383-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 05/10/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
Norovirus is a leading cause of epidemic acute gastroenteritis. More than 30 genotypes circulate in humans, some are common, and others are only sporadically detected. Here, we investigated whether serology can be used to determine which genotypes infect children. We established a multiplex protein microarray with structural and non-structural norovirus antigens that allowed simultaneous antibody testing against 30 human GI and GII genotypes. Antibody responses of sera obtained from 287 children aged < 1 month to 5.5 years were profiled. Most specific IgG and IgA responses were directed against the GII.2, GII.3, GII.4, and GII.6 capsid genotypes. While we detected antibody responses against rare genotypes, we found no evidence for wide circulation. We also detected genotype-specific antibodies against the non-structural proteins p48 and p22 in sera of older children. In this study, we show the age-dependent antibody responses to a broad range of norovirus capsid and polymerase genotypes, which will aid in the development of vaccines.
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Affiliation(s)
- Nele Villabruna
- Department of Viroscience, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Ray W Izquierdo-Lara
- Department of Viroscience, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | | | - Erwin de Bruin
- Department of Viroscience, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Felicity Chandler
- Department of Viroscience, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Tran Thi Nhu Thao
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Brenda M Westerhuis
- Department of Viroscience, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Janko van Beek
- Department of Viroscience, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Louise Sigfrid
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Carlo Giaquinto
- Division of Paediatric Infectious Diseases, Department of Women's and Children's Health, University Hospital of Padua, Padua, Italy
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Julia A Bielicki
- Paediatric Infectious Disease Research Group, Institute for Infection and Immunity, St George's University of London, London, UK.,Department of Infectious Diseases and Vaccinology, University of Basel Children's Hospital (UKBB), Basel, Switzerland
| | - Malte Kohns Vasconcelos
- Paediatric Infectious Disease Research Group, Institute for Infection and Immunity, St George's University of London, London, UK.,Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Marion P G Koopmans
- Department of Viroscience, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
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40
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Sanders JSF, Messchendorp AL, de Vries RD, Baan CC, van Baarle D, van Binnendijk R, Diavatopoulos DA, Geers D, Schmitz KS, GeurtsvanKessel CH, den Hartog G, Kho MML, Koopmans MPG, van der Molen RG, Remmerswaal EBM, Rots N, Gansevoort RT, Bemelman FJ, Hilbrands LB, Reinders MEJ. Antibody and T-Cell Responses 6 Months After Coronavirus Disease 2019 Messenger RNA-1273 Vaccination in Patients With Chronic Kidney Disease, on Dialysis, or Living With a Kidney Transplant. Clin Infect Dis 2022; 76:e188-e199. [PMID: 35796536 PMCID: PMC9278186 DOI: 10.1093/cid/ciac557] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/23/2022] [Accepted: 06/30/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The immune response to COVID-19 vaccination is inferior in kidney transplant recipients (KTRs) and to a lesser extent in patients on dialysis or with chronic kidney disease (CKD). We assessed the immune response 6 months after mRNA-1273 vaccination in kidney patients and compared this to controls. METHODS A total of 152 participants with CKD stages G4/5 (eGFR <30 mL/min/1.73 m2), 145 participants on dialysis, 267 KTRs, and 181 controls were included. SARS-CoV-2 Spike S1 specific IgG antibodies were measured using fluorescent bead-based multiplex-immunoassay, neutralizing antibodies to ancestral, Delta, and Omicron (BA.1) variants by plaque reduction, and T-cell responses by interferon-γ release assay. RESULTS At 6 months after vaccination, S1-specific antibodies were detected in 100% of controls, 98.7% of CKD G4/5 patients, 95.1% of dialysis patients, and 56.6% of KTRs. These figures were comparable to the response rates at 28 days, but antibody levels waned significantly. Neutralization of the ancestral and Delta variants was detected in most participants, whereas neutralization of Omicron was mostly absent. S-specific T-cell responses were detected at 6 months in 75.0% of controls, 69.4% of CKD G4/5 patients, 52.6% of dialysis patients, and 12.9% of KTRs. T-cell responses at 6 months were significantly lower than responses at 28 days. CONCLUSIONS Although seropositivity rates at 6 months were comparable to rates at 28 days after vaccination, significantly decreased antibody levels and T-cell responses were observed. The combination of low antibody levels, reduced T-cell responses, and absent neutralization of the newly emerging variants indicates the need for additional boosts or alternative vaccination strategies in KTRs. CLINICAL TRIALS REGISTRATION NCT04741386.
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Affiliation(s)
- Jan-Stephan F Sanders
- Correspondence: J-S. F. Sanders, Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, Groningen, The Netherlands ()
| | | | | | - Carla C Baan
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus MC Transplant Institute, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Debbie van Baarle
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, Groningen, The Netherlands,Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Rob van Binnendijk
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Dimitri A Diavatopoulos
- Radboud Center for Infectious Diseases, Radboud University Medical Center Nijmegen, Nijmegen, The Netherlands,Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen, Nijmegen, The Netherlands
| | - Daryl Geers
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Katharina S Schmitz
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Gerco den Hartog
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Marcia M L Kho
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus MC Transplant Institute, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Renate G van der Molen
- Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen, Nijmegen, The Netherlands
| | - Ester B M Remmerswaal
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Nynke Rots
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Ron T Gansevoort
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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41
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Nieuwenhuijse DF, van der Linden A, Kohl RHG, Sikkema RS, Koopmans MPG, Oude Munnink BB. Towards reliable whole genome sequencing for outbreak preparedness and response. BMC Genomics 2022; 23:569. [PMID: 35945497 PMCID: PMC9361258 DOI: 10.1186/s12864-022-08749-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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] [Received: 12/13/2021] [Accepted: 07/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To understand the dynamics of infectious diseases, genomic epidemiology is increasingly advocated, with a need for rapid generation of genetic sequences during outbreaks for public health decision making. Here, we explore the use of metagenomic sequencing compared to specific amplicon- and capture-based sequencing, both on the Nanopore and the Illumina platform for generation of whole genomes of Usutu virus, Zika virus, West Nile virus, and Yellow Fever virus. RESULTS We show that amplicon-based Nanopore sequencing can be used to rapidly obtain whole genome sequences in samples with a viral load up to Ct 33 and capture-based Illumina is the most sensitive method for initial virus determination. CONCLUSIONS The choice of sequencing approach and platform is important for laboratories wishing to start whole genome sequencing. Depending on the purpose of genome sequencing the best choice can differ. The insights presented in this work and the shown differences in data characteristics can guide labs to make a well informed choice.
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Affiliation(s)
| | | | - Robert H G Kohl
- Departement of Virology of the Vaccination Programme, RIVM, Bilthoven, the Netherlands
| | - Reina S Sikkema
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Bas B Oude Munnink
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands.
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42
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Sablerolles RSG, Rietdijk WJR, Goorhuis A, Postma DF, Visser LG, Schmitz KS, Geers D, Bogers S, van Haren E, Koopmans MPG, Dalm VASH, Kootstra NA, Huckriede ALW, Akkerman R, Beukema M, Lafeber M, van Baarle D, de Vries RD, van der Kuy PHM, GeurtsvanKessel CH. Durability of Immune Responses After Boosting in Ad26.COV2.S-Primed Healthcare Workers. Clin Infect Dis 2022; 76:e533-e536. [PMID: 35723273 PMCID: PMC9384313 DOI: 10.1093/cid/ciac495] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 04/15/2022] [Revised: 06/06/2022] [Accepted: 06/10/2022] [Indexed: 11/14/2022] Open
Abstract
The emergence of SARS-CoV-2 variants raised questions regarding the durability of immune responses after homologous or heterologous boosters after Ad26.COV2.S-priming. We found that SARS-CoV-2-specific binding antibodies, neutralizing antibodies, and T cells are detectable 5 months after boosting, although waning of antibodies and limited cross-reactivity with Omicron BA.1 was observed.
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Affiliation(s)
| | | | - Abraham Goorhuis
- Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Amsterdam University Medical Centers, Amsterdam, The Netherlands,Infection & Immunity, Amsterdam Public Health, University of Amsterdam, Amsterdam, The Netherlands
| | - Douwe F Postma
- Department of Internal Medicine and Infectious Diseases, University Medical Center Groningen, Groningen, The Netherlands
| | - Leo G Visser
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Katharina S Schmitz
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Daryl Geers
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Susanne Bogers
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Eva van Haren
- Department of Hospital Pharmacy, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Virgil A S H Dalm
- Department of Internal Medicine, Division of Allergy & Clinical Immunology and Department of Immunology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Neeltje A Kootstra
- Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Infection and Immunity Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - Anke L W Huckriede
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Renate Akkerman
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Martin Beukema
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Melvin Lafeber
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Debbie van Baarle
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands,Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | | | | | - Corine H GeurtsvanKessel
- Correspondence: C. H. GeurtsvanKessel, Department of Viroscience, Erasmus Medical Center, 3015GD, Rotterdam, The Netherlands ()
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43
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Rissmann M, Noack D, van Riel D, Schmitz KS, de Vries RD, van Run P, Lamers MM, GeurtsvanKessel CH, Koopmans MPG, Fouchier RAM, Kuiken T, Haagmans BL, Rockx B. Pulmonary lesions following inoculation with the SARS-CoV-2 Omicron BA.1 (B.1.1.529) variant in Syrian golden hamsters. Emerg Microbes Infect 2022; 11:1778-1786. [PMID: 35787236 PMCID: PMC9295819 DOI: 10.1080/22221751.2022.2095932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
AbstractThe Omicron BA.1 (B.1.1.529) SARS-CoV-2 variant is characterized by a high number of mutations in the viral genome, associated with immune-escape and increased viral spread. It remains unclear whether milder COVID-19 disease progression observed after infection with Omicron BA.1 in humans is due to reduced pathogenicity of the virus or due to pre-existing immunity from vaccination or previous infection. Here, we inoculated hamsters with Omicron BA.1 to evaluate pathogenicity and kinetics of viral shedding, compared to Delta (B.1.617.2) and to animals re-challenged with Omicron BA.1 after previous SARS-CoV-2 614G infection. Omicron BA.1 infected animals showed reduced clinical signs, pathological changes, and viral shedding, compared to Delta-infected animals, but still showed gross- and histopathological evidence of pneumonia. Pre-existing immunity reduced viral shedding and protected against pneumonia. Our data indicate that the observed decrease of disease severity is in part due to intrinsic properties of the Omicron BA.1 variant.
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Affiliation(s)
- Melanie Rissmann
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Danny Noack
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Debby van Riel
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Katharina S Schmitz
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Rory D de Vries
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Peter van Run
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Mart M Lamers
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Marion P G Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Thijs Kuiken
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Barry Rockx
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
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44
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Noack D, Travar M, Mrdjen V, Voermans JJC, van de Vijver D, Molenkamp R, Koopmans MPG, Goeijenbier M, Rockx B. Serum Markers Associated with Disease Severity in a Bosnian Hemorrhagic Fever with Renal Syndrome Cohort. Viruses 2022; 14:v14071377. [PMID: 35891358 PMCID: PMC9316913 DOI: 10.3390/v14071377] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/10/2022] [Accepted: 06/22/2022] [Indexed: 12/10/2022] Open
Abstract
Puumala orthohantavirus (PUUV) is endemic in Europe and can cause hemorrhagic fever with renal syndrome (nephropathia epidemica). Disease features include fever, thrombocytopenia, and acute kidney injury (AKI). This retrospective cohort study of forty PUUV patients aims to characterize associations of serum immunological, hemostatic or kidney injury markers to disease severity. While interleukin-18 (IL-18) was significantly increased in severely thrombocytopenic patients (<100 × 109 platelets/L) compared to patients with higher platelet counts, RANTES was significantly decreased in these patients. These data suggest that patients with significant thrombocytopenia might have experienced pronounced Th1 immune responses. When kidney dysfunction was used as the primary disease outcome, recently identified AKI biomarkers (Cystatin C, insulin-like growth factor-binding protein 7, Nephrin, and trefoil factor 3) were significantly upregulated in patients with severe PUUV infection, defined as the estimated glomerular filtration rate (eGFR) below 30 m/min/1.73 m2. The increased expression of these markers specifically indicates pathology in glomeruli and proximal tubuli. Furthermore, E-selectin was significantly higher while interferon gamma-induced protein 10 (IP-10) was significantly lower in PUUV patients with more severe kidney dysfunction compared to patients with higher eGFR-values. Increased E-selectin illustrates the central role of endothelial cell activation, whereas decreased IP-10 could indicate a less important role of this cytokine in the pathogenesis of kidney dysfunction.
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Affiliation(s)
- Danny Noack
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (D.N.); (J.J.C.V.); (D.v.d.V.); (R.M.); (M.P.G.K.); (M.G.)
| | - Maja Travar
- Department for Clinical Microbiology, University Clinical Center of Republika Srpska, 78000 Banja Luka, Bosnia and Herzegovina; (M.T.); (V.M.)
- Department for Microbiology and Immunology, Faculty of Medicine, University of Banja Luka, 78000 Banja Luka, Republika Srpska, Bosnia and Herzegovina
| | - Visnja Mrdjen
- Department for Clinical Microbiology, University Clinical Center of Republika Srpska, 78000 Banja Luka, Bosnia and Herzegovina; (M.T.); (V.M.)
- Department for Microbiology and Immunology, Faculty of Medicine, University of Banja Luka, 78000 Banja Luka, Republika Srpska, Bosnia and Herzegovina
| | - Jolanda J. C. Voermans
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (D.N.); (J.J.C.V.); (D.v.d.V.); (R.M.); (M.P.G.K.); (M.G.)
| | - David van de Vijver
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (D.N.); (J.J.C.V.); (D.v.d.V.); (R.M.); (M.P.G.K.); (M.G.)
| | - Richard Molenkamp
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (D.N.); (J.J.C.V.); (D.v.d.V.); (R.M.); (M.P.G.K.); (M.G.)
| | - Marion P. G. Koopmans
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (D.N.); (J.J.C.V.); (D.v.d.V.); (R.M.); (M.P.G.K.); (M.G.)
| | - Marco Goeijenbier
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (D.N.); (J.J.C.V.); (D.v.d.V.); (R.M.); (M.P.G.K.); (M.G.)
- Department of Intensive Care, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Barry Rockx
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (D.N.); (J.J.C.V.); (D.v.d.V.); (R.M.); (M.P.G.K.); (M.G.)
- Correspondence:
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Adisasmito WB, Almuhairi S, Behravesh CB, Bilivogui P, Bukachi SA, Casas N, Cediel Becerra N, Charron DF, Chaudhary A, Ciacci Zanella JR, Cunningham AA, Dar O, Debnath N, Dungu B, Farag E, Gao GF, Hayman DTS, Khaitsa M, Koopmans MPG, Machalaba C, Mackenzie JS, Markotter W, Mettenleiter TC, Morand S, Smolenskiy V, Zhou L. One Health: A new definition for a sustainable and healthy future. PLoS Pathog 2022; 18:e1010537. [PMID: 35737670 PMCID: PMC9223325 DOI: 10.1371/journal.ppat.1010537] [Citation(s) in RCA: 119] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
| | | | - Salama Almuhairi
- National Emergency Crisis and Disasters Management Authority, Abu Dhabi, United Arab Emirates
| | | | - Pépé Bilivogui
- World Health Organization, Guinea Country Office, Conakry, Guinea
| | - Salome A. Bukachi
- Institute of Anthropology, Gender and African Studies, University of Nairobi, Nairobi, Kenya
| | - Natalia Casas
- National Ministry of Health, Autonomous City of Buenos Aires, Argentina
| | | | | | | | - Janice R. Ciacci Zanella
- Brazilian Agricultural Research Corporation (Embrapa), Embrapa Swine and Poultry, Concórdia, Santa Catarina, Brazil
| | | | - Osman Dar
- Global Operations Division, United Kingdom Health Security Agency, London, United Kingdom
- Global Health Programme, Chatham House, Royal Institute of International Affairs, London, United Kingdom
| | - Nitish Debnath
- Fleming Fund Country Grant to Bangladesh, DAI Global, Dhaka, Bangladesh
| | - Baptiste Dungu
- Afrivet B M, Pretoria, South Africa
- Faculty of Veterinary Science, University of Kinshasa, Kinshasa, Democratic Republic Congo
| | - Elmoubasher Farag
- Ministry of Public Health, Health Protection & Communicable Diseases Division, Doha, Qatar
| | - George F. Gao
- Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - David T. S. Hayman
- Molecular Epidemiology and Public Health Laboratory, Massey University, Palmerston North, New Zealand
| | - Margaret Khaitsa
- Mississippi State University, Starkville, Mississippi, United States of America
| | | | | | - John S. Mackenzie
- Faculty of Health Sciences, Curtin University, Perth
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Wanda Markotter
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- * E-mail: (WM); (TCM)
| | - Thomas C. Mettenleiter
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
- * E-mail: (WM); (TCM)
| | - Serge Morand
- MIVEGEC, CNRS-IRD-Montpellier Université, Montpellier, France; Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand
| | - Vyacheslav Smolenskiy
- Federal Service for Surveillance on Consumer Rights Protection and Human Well-being (Rospotrebnadzor), Moscow, Russian Federation
| | - Lei Zhou
- Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
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46
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DeGrace MM, Ghedin E, Frieman MB, Krammer F, Grifoni A, Alisoltani A, Alter G, Amara RR, Baric RS, Barouch DH, Bloom JD, Bloyet LM, Bonenfant G, Boon ACM, Boritz EA, Bratt DL, Bricker TL, Brown L, Buchser WJ, Carreño JM, Cohen-Lavi L, Darling TL, Davis-Gardner ME, Dearlove BL, Di H, Dittmann M, Doria-Rose NA, Douek DC, Drosten C, Edara VV, Ellebedy A, Fabrizio TP, Ferrari G, Fischer WM, Florence WC, Fouchier RAM, Franks J, García-Sastre A, Godzik A, Gonzalez-Reiche AS, Gordon A, Haagmans BL, Halfmann PJ, Ho DD, Holbrook MR, Huang Y, James SL, Jaroszewski L, Jeevan T, Johnson RM, Jones TC, Joshi A, Kawaoka Y, Kercher L, Koopmans MPG, Korber B, Koren E, Koup RA, LeGresley EB, Lemieux JE, Liebeskind MJ, Liu Z, Livingston B, Logue JP, Luo Y, McDermott AB, McElrath MJ, Meliopoulos VA, Menachery VD, Montefiori DC, Mühlemann B, Munster VJ, Munt JE, Nair MS, Netzl A, Niewiadomska AM, O'Dell S, Pekosz A, Perlman S, Pontelli MC, Rockx B, Rolland M, Rothlauf PW, Sacharen S, Scheuermann RH, Schmidt SD, Schotsaert M, Schultz-Cherry S, Seder RA, Sedova M, Sette A, Shabman RS, Shen X, Shi PY, Shukla M, Simon V, Stumpf S, Sullivan NJ, Thackray LB, Theiler J, Thomas PG, Trifkovic S, Türeli S, Turner SA, Vakaki MA, van Bakel H, VanBlargan LA, Vincent LR, Wallace ZS, Wang L, Wang M, Wang P, Wang W, Weaver SC, Webby RJ, Weiss CD, Wentworth DE, Weston SM, Whelan SPJ, Whitener BM, Wilks SH, Xie X, Ying B, Yoon H, Zhou B, Hertz T, Smith DJ, Diamond MS, Post DJ, Suthar MS. Defining the risk of SARS-CoV-2 variants on immune protection. Nature 2022; 605:640-652. [PMID: 35361968 PMCID: PMC9345323 DOI: 10.1038/s41586-022-04690-5] [Citation(s) in RCA: 93] [Impact Index Per Article: 46.5] [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: 11/25/2021] [Accepted: 03/24/2022] [Indexed: 11/09/2022]
Abstract
The global emergence of many severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants jeopardizes the protective antiviral immunity induced after infection or vaccination. To address the public health threat caused by the increasing SARS-CoV-2 genomic diversity, the National Institute of Allergy and Infectious Diseases within the National Institutes of Health established the SARS-CoV-2 Assessment of Viral Evolution (SAVE) programme. This effort was designed to provide a real-time risk assessment of SARS-CoV-2 variants that could potentially affect the transmission, virulence, and resistance to infection- and vaccine-induced immunity. The SAVE programme is a critical data-generating component of the US Government SARS-CoV-2 Interagency Group to assess implications of SARS-CoV-2 variants on diagnostics, vaccines and therapeutics, and for communicating public health risk. Here we describe the coordinated approach used to identify and curate data about emerging variants, their impact on immunity and effects on vaccine protection using animal models. We report the development of reagents, methodologies, models and notable findings facilitated by this collaborative approach and identify future challenges. This programme is a template for the response to rapidly evolving pathogens with pandemic potential by monitoring viral evolution in the human population to identify variants that could reduce the effectiveness of countermeasures.
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Affiliation(s)
- Marciela M DeGrace
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Elodie Ghedin
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institutes of Health, Rockville, MD, USA
| | - Matthew B Frieman
- Center for Pathogen Research, Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, MD, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Boston, MA, USA
| | - Rama R Amara
- Department of Microbiology and Immunology, Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jesse D Bloom
- Fred Hutch Cancer Center, Howard Hughes Medical Institute, Seattle, WA, USA
| | - Louis-Marie Bloyet
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Gaston Bonenfant
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Adrianus C M Boon
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Eli A Boritz
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Debbie L Bratt
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- CAMRIS, Contractor for NIAID, Bethesda, MD, USA
| | - Traci L Bricker
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Liliana Brown
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - William J Buchser
- High Throughput Screening Center, Washington University School of Medicine, St Louis, MO, USA
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Liel Cohen-Lavi
- National Institute for Biotechnology in the Negev, Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
| | - Tamarand L Darling
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Meredith E Davis-Gardner
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Bethany L Dearlove
- US Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Han Di
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Meike Dittmann
- Microbiology Department, New York University Grossman School of Medicine, New York, NY, USA
| | - Nicole A Doria-Rose
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Daniel C Douek
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin and German Center for Infection Research (DZIF), Berlin, Germany
| | - Venkata-Viswanadh Edara
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Ali Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Thomas P Fabrizio
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Guido Ferrari
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Will M Fischer
- Los Alamos National Laboratory, New Mexico Consortium, Los Alamos, NM, USA
| | - William C Florence
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | | | - John Franks
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adam Godzik
- University of California Riverside School of Medicine, Riverside, CA, USA
| | - Ana Silvia Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aubree Gordon
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Bart L Haagmans
- Department Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Michael R Holbrook
- National Institute of Allergy and Infectious Diseases Integrated Research Facility, Frederick, MD, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Sarah L James
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Lukasz Jaroszewski
- University of California Riverside School of Medicine, Riverside, CA, USA
| | - Trushar Jeevan
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert M Johnson
- Center for Pathogen Research, Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, MD, USA
| | - Terry C Jones
- Institute of Virology, Charité-Universitätsmedizin and German Center for Infection Research (DZIF), Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Astha Joshi
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, Tokyo, Japan
| | - Lisa Kercher
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Bette Korber
- Los Alamos National Laboratory, New Mexico Consortium, Los Alamos, NM, USA
| | - Eilay Koren
- National Institute for Biotechnology in the Negev, Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
- The Shraga Segal Department of Microbiology and Immunology, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Richard A Koup
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Eric B LeGresley
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - Mariel J Liebeskind
- High Throughput Screening Center, Washington University School of Medicine, St Louis, MO, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Brandi Livingston
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - James P Logue
- Center for Pathogen Research, Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yang Luo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Adrian B McDermott
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | | | - Victoria A Meliopoulos
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Vineet D Menachery
- Department of Microbiology and Immunology, Institute for Human Infection and Immunity, World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | | | - Barbara Mühlemann
- Institute of Virology, Charité-Universitätsmedizin and German Center for Infection Research (DZIF), Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Vincent J Munster
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Jenny E Munt
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Manoj S Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Antonia Netzl
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - Sijy O'Dell
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Andrew Pekosz
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Marjorie C Pontelli
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Barry Rockx
- Department Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Morgane Rolland
- US Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Paul W Rothlauf
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Sinai Sacharen
- National Institute for Biotechnology in the Negev, Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
- The Shraga Segal Department of Microbiology and Immunology, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | | | - Stephen D Schmidt
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert A Seder
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Mayya Sedova
- University of California Riverside School of Medicine, Riverside, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Reed S Shabman
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Xiaoying Shen
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Maulik Shukla
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Data Science and Learning Division, Argonne National Laboratory, Argonne, IL, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Spencer Stumpf
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Nancy J Sullivan
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Larissa B Thackray
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - James Theiler
- Los Alamos National Laboratory, New Mexico Consortium, Los Alamos, NM, USA
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Sanja Trifkovic
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Sina Türeli
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Samuel A Turner
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Maria A Vakaki
- High Throughput Screening Center, Washington University School of Medicine, St Louis, MO, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura A VanBlargan
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Leah R Vincent
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Zachary S Wallace
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Li Wang
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Maple Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Wei Wang
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Scott C Weaver
- Department of Microbiology and Immunology, Institute for Human Infection and Immunity, World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Richard J Webby
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Carol D Weiss
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - David E Wentworth
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stuart M Weston
- Center for Pathogen Research, Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Bradley M Whitener
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Samuel H Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Baoling Ying
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Hyejin Yoon
- Los Alamos National Laboratory, New Mexico Consortium, Los Alamos, NM, USA
| | - Bin Zhou
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Tomer Hertz
- Department of Microbiology, Immunology and Genetics Faculty of Health Sciences Ben-Gurion University of the Negev, Be'er Sheva, Israel.
| | - Derek J Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK.
| | - Michael S Diamond
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA.
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA.
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA.
| | - Diane J Post
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
| | - Mehul S Suthar
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA.
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Affiliation(s)
- Bart L Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands; Pandemic and Disaster Preparedness Centre, Rotterdam, Netherlands.
| | - Marion P G Koopmans
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands; Pandemic and Disaster Preparedness Centre, Rotterdam, Netherlands
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48
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Sablerolles RSG, Rietdijk WJR, Goorhuis A, Postma DF, Visser LG, Geers D, Schmitz KS, Garcia Garrido HM, Koopmans MPG, Dalm VASH, Kootstra NA, Huckriede ALW, Lafeber M, van Baarle D, GeurtsvanKessel CH, de Vries RD, van der Kuy PHM. Immunogenicity and Reactogenicity of Vaccine Boosters after Ad26.COV2.S Priming. N Engl J Med 2022; 386:951-963. [PMID: 35045226 PMCID: PMC8796791 DOI: 10.1056/nejmoa2116747] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND The Ad26.COV2.S vaccine, which was approved as a single-shot immunization regimen, has been shown to be effective against severe coronavirus disease 2019. However, this vaccine induces lower severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein (S)-specific antibody levels than those induced by messenger RNA (mRNA)-based vaccines. The immunogenicity and reactogenicity of a homologous or heterologous booster in persons who have received an Ad26.COV2.S priming dose are unclear. METHODS In this single-blind, multicenter, randomized, controlled trial involving health care workers who had received a priming dose of Ad26.COV2.S vaccine, we assessed immunogenicity and reactogenicity 28 days after a homologous or heterologous booster vaccination. The participants were assigned to receive no booster, an Ad26.COV2.S booster, an mRNA-1273 booster, or a BNT162b2 booster. The primary end point was the level of S-specific binding antibodies, and the secondary end points were the levels of neutralizing antibodies, S-specific T-cell responses, and reactogenicity. A post hoc analysis was performed to compare mRNA-1273 boosting with BNT162b2 boosting. RESULTS Homologous or heterologous booster vaccination resulted in higher levels of S-specific binding antibodies, neutralizing antibodies, and T-cell responses than a single Ad26.COV2.S vaccination. The increase in binding antibodies was significantly larger with heterologous regimens that included mRNA-based vaccines than with the homologous booster. The mRNA-1273 booster was most immunogenic and was associated with higher reactogenicity than the BNT162b2 and Ad26.COV2.S boosters. Local and systemic reactions were generally mild to moderate in the first 2 days after booster administration. CONCLUSIONS The Ad26.COV2.S and mRNA boosters had an acceptable safety profile and were immunogenic in health care workers who had received a priming dose of Ad26.COV2.S vaccine. The strongest responses occurred after boosting with mRNA-based vaccines. Boosting with any available vaccine was better than not boosting. (Funded by the Netherlands Organization for Health Research and Development ZonMw; SWITCH ClinicalTrials.gov number, NCT04927936.).
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Affiliation(s)
- Roos S G Sablerolles
- From the Departments of Internal Medicine (R.S.G.S., M.L.), Hospital Pharmacy (R.S.G.S., W.J.R.R., P.H.M.K.), and Viroscience (D.G., K.S.S., M.P.G.K., C.H.G., R.D.V.) and the Department of Internal Medicine, Division of Allergy and Clinical Immunology, and Department of Immunology (V.A.S.H.D.), Erasmus University Medical Center, Rotterdam, the Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases (A.G., H.M.G.G.), and the Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam (N.A.K.), Amsterdam, the Department of Internal Medicine and Infectious Diseases (D.F.P.), and the Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen (A.L.W.H., D.B.), Groningen, the Department of Infectious Diseases, Leiden University Medical Center, Leiden (L.G.V.), and the Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven (D.B.) - all in the Netherlands
| | - Wim J R Rietdijk
- From the Departments of Internal Medicine (R.S.G.S., M.L.), Hospital Pharmacy (R.S.G.S., W.J.R.R., P.H.M.K.), and Viroscience (D.G., K.S.S., M.P.G.K., C.H.G., R.D.V.) and the Department of Internal Medicine, Division of Allergy and Clinical Immunology, and Department of Immunology (V.A.S.H.D.), Erasmus University Medical Center, Rotterdam, the Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases (A.G., H.M.G.G.), and the Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam (N.A.K.), Amsterdam, the Department of Internal Medicine and Infectious Diseases (D.F.P.), and the Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen (A.L.W.H., D.B.), Groningen, the Department of Infectious Diseases, Leiden University Medical Center, Leiden (L.G.V.), and the Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven (D.B.) - all in the Netherlands
| | - Abraham Goorhuis
- From the Departments of Internal Medicine (R.S.G.S., M.L.), Hospital Pharmacy (R.S.G.S., W.J.R.R., P.H.M.K.), and Viroscience (D.G., K.S.S., M.P.G.K., C.H.G., R.D.V.) and the Department of Internal Medicine, Division of Allergy and Clinical Immunology, and Department of Immunology (V.A.S.H.D.), Erasmus University Medical Center, Rotterdam, the Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases (A.G., H.M.G.G.), and the Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam (N.A.K.), Amsterdam, the Department of Internal Medicine and Infectious Diseases (D.F.P.), and the Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen (A.L.W.H., D.B.), Groningen, the Department of Infectious Diseases, Leiden University Medical Center, Leiden (L.G.V.), and the Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven (D.B.) - all in the Netherlands
| | - Douwe F Postma
- From the Departments of Internal Medicine (R.S.G.S., M.L.), Hospital Pharmacy (R.S.G.S., W.J.R.R., P.H.M.K.), and Viroscience (D.G., K.S.S., M.P.G.K., C.H.G., R.D.V.) and the Department of Internal Medicine, Division of Allergy and Clinical Immunology, and Department of Immunology (V.A.S.H.D.), Erasmus University Medical Center, Rotterdam, the Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases (A.G., H.M.G.G.), and the Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam (N.A.K.), Amsterdam, the Department of Internal Medicine and Infectious Diseases (D.F.P.), and the Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen (A.L.W.H., D.B.), Groningen, the Department of Infectious Diseases, Leiden University Medical Center, Leiden (L.G.V.), and the Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven (D.B.) - all in the Netherlands
| | - Leo G Visser
- From the Departments of Internal Medicine (R.S.G.S., M.L.), Hospital Pharmacy (R.S.G.S., W.J.R.R., P.H.M.K.), and Viroscience (D.G., K.S.S., M.P.G.K., C.H.G., R.D.V.) and the Department of Internal Medicine, Division of Allergy and Clinical Immunology, and Department of Immunology (V.A.S.H.D.), Erasmus University Medical Center, Rotterdam, the Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases (A.G., H.M.G.G.), and the Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam (N.A.K.), Amsterdam, the Department of Internal Medicine and Infectious Diseases (D.F.P.), and the Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen (A.L.W.H., D.B.), Groningen, the Department of Infectious Diseases, Leiden University Medical Center, Leiden (L.G.V.), and the Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven (D.B.) - all in the Netherlands
| | - Daryl Geers
- From the Departments of Internal Medicine (R.S.G.S., M.L.), Hospital Pharmacy (R.S.G.S., W.J.R.R., P.H.M.K.), and Viroscience (D.G., K.S.S., M.P.G.K., C.H.G., R.D.V.) and the Department of Internal Medicine, Division of Allergy and Clinical Immunology, and Department of Immunology (V.A.S.H.D.), Erasmus University Medical Center, Rotterdam, the Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases (A.G., H.M.G.G.), and the Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam (N.A.K.), Amsterdam, the Department of Internal Medicine and Infectious Diseases (D.F.P.), and the Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen (A.L.W.H., D.B.), Groningen, the Department of Infectious Diseases, Leiden University Medical Center, Leiden (L.G.V.), and the Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven (D.B.) - all in the Netherlands
| | - Katharina S Schmitz
- From the Departments of Internal Medicine (R.S.G.S., M.L.), Hospital Pharmacy (R.S.G.S., W.J.R.R., P.H.M.K.), and Viroscience (D.G., K.S.S., M.P.G.K., C.H.G., R.D.V.) and the Department of Internal Medicine, Division of Allergy and Clinical Immunology, and Department of Immunology (V.A.S.H.D.), Erasmus University Medical Center, Rotterdam, the Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases (A.G., H.M.G.G.), and the Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam (N.A.K.), Amsterdam, the Department of Internal Medicine and Infectious Diseases (D.F.P.), and the Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen (A.L.W.H., D.B.), Groningen, the Department of Infectious Diseases, Leiden University Medical Center, Leiden (L.G.V.), and the Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven (D.B.) - all in the Netherlands
| | - Hannah M Garcia Garrido
- From the Departments of Internal Medicine (R.S.G.S., M.L.), Hospital Pharmacy (R.S.G.S., W.J.R.R., P.H.M.K.), and Viroscience (D.G., K.S.S., M.P.G.K., C.H.G., R.D.V.) and the Department of Internal Medicine, Division of Allergy and Clinical Immunology, and Department of Immunology (V.A.S.H.D.), Erasmus University Medical Center, Rotterdam, the Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases (A.G., H.M.G.G.), and the Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam (N.A.K.), Amsterdam, the Department of Internal Medicine and Infectious Diseases (D.F.P.), and the Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen (A.L.W.H., D.B.), Groningen, the Department of Infectious Diseases, Leiden University Medical Center, Leiden (L.G.V.), and the Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven (D.B.) - all in the Netherlands
| | - Marion P G Koopmans
- From the Departments of Internal Medicine (R.S.G.S., M.L.), Hospital Pharmacy (R.S.G.S., W.J.R.R., P.H.M.K.), and Viroscience (D.G., K.S.S., M.P.G.K., C.H.G., R.D.V.) and the Department of Internal Medicine, Division of Allergy and Clinical Immunology, and Department of Immunology (V.A.S.H.D.), Erasmus University Medical Center, Rotterdam, the Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases (A.G., H.M.G.G.), and the Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam (N.A.K.), Amsterdam, the Department of Internal Medicine and Infectious Diseases (D.F.P.), and the Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen (A.L.W.H., D.B.), Groningen, the Department of Infectious Diseases, Leiden University Medical Center, Leiden (L.G.V.), and the Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven (D.B.) - all in the Netherlands
| | - Virgil A S H Dalm
- From the Departments of Internal Medicine (R.S.G.S., M.L.), Hospital Pharmacy (R.S.G.S., W.J.R.R., P.H.M.K.), and Viroscience (D.G., K.S.S., M.P.G.K., C.H.G., R.D.V.) and the Department of Internal Medicine, Division of Allergy and Clinical Immunology, and Department of Immunology (V.A.S.H.D.), Erasmus University Medical Center, Rotterdam, the Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases (A.G., H.M.G.G.), and the Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam (N.A.K.), Amsterdam, the Department of Internal Medicine and Infectious Diseases (D.F.P.), and the Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen (A.L.W.H., D.B.), Groningen, the Department of Infectious Diseases, Leiden University Medical Center, Leiden (L.G.V.), and the Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven (D.B.) - all in the Netherlands
| | - Neeltje A Kootstra
- From the Departments of Internal Medicine (R.S.G.S., M.L.), Hospital Pharmacy (R.S.G.S., W.J.R.R., P.H.M.K.), and Viroscience (D.G., K.S.S., M.P.G.K., C.H.G., R.D.V.) and the Department of Internal Medicine, Division of Allergy and Clinical Immunology, and Department of Immunology (V.A.S.H.D.), Erasmus University Medical Center, Rotterdam, the Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases (A.G., H.M.G.G.), and the Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam (N.A.K.), Amsterdam, the Department of Internal Medicine and Infectious Diseases (D.F.P.), and the Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen (A.L.W.H., D.B.), Groningen, the Department of Infectious Diseases, Leiden University Medical Center, Leiden (L.G.V.), and the Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven (D.B.) - all in the Netherlands
| | - Anke L W Huckriede
- From the Departments of Internal Medicine (R.S.G.S., M.L.), Hospital Pharmacy (R.S.G.S., W.J.R.R., P.H.M.K.), and Viroscience (D.G., K.S.S., M.P.G.K., C.H.G., R.D.V.) and the Department of Internal Medicine, Division of Allergy and Clinical Immunology, and Department of Immunology (V.A.S.H.D.), Erasmus University Medical Center, Rotterdam, the Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases (A.G., H.M.G.G.), and the Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam (N.A.K.), Amsterdam, the Department of Internal Medicine and Infectious Diseases (D.F.P.), and the Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen (A.L.W.H., D.B.), Groningen, the Department of Infectious Diseases, Leiden University Medical Center, Leiden (L.G.V.), and the Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven (D.B.) - all in the Netherlands
| | - Melvin Lafeber
- From the Departments of Internal Medicine (R.S.G.S., M.L.), Hospital Pharmacy (R.S.G.S., W.J.R.R., P.H.M.K.), and Viroscience (D.G., K.S.S., M.P.G.K., C.H.G., R.D.V.) and the Department of Internal Medicine, Division of Allergy and Clinical Immunology, and Department of Immunology (V.A.S.H.D.), Erasmus University Medical Center, Rotterdam, the Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases (A.G., H.M.G.G.), and the Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam (N.A.K.), Amsterdam, the Department of Internal Medicine and Infectious Diseases (D.F.P.), and the Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen (A.L.W.H., D.B.), Groningen, the Department of Infectious Diseases, Leiden University Medical Center, Leiden (L.G.V.), and the Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven (D.B.) - all in the Netherlands
| | - Debbie van Baarle
- From the Departments of Internal Medicine (R.S.G.S., M.L.), Hospital Pharmacy (R.S.G.S., W.J.R.R., P.H.M.K.), and Viroscience (D.G., K.S.S., M.P.G.K., C.H.G., R.D.V.) and the Department of Internal Medicine, Division of Allergy and Clinical Immunology, and Department of Immunology (V.A.S.H.D.), Erasmus University Medical Center, Rotterdam, the Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases (A.G., H.M.G.G.), and the Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam (N.A.K.), Amsterdam, the Department of Internal Medicine and Infectious Diseases (D.F.P.), and the Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen (A.L.W.H., D.B.), Groningen, the Department of Infectious Diseases, Leiden University Medical Center, Leiden (L.G.V.), and the Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven (D.B.) - all in the Netherlands
| | - Corine H GeurtsvanKessel
- From the Departments of Internal Medicine (R.S.G.S., M.L.), Hospital Pharmacy (R.S.G.S., W.J.R.R., P.H.M.K.), and Viroscience (D.G., K.S.S., M.P.G.K., C.H.G., R.D.V.) and the Department of Internal Medicine, Division of Allergy and Clinical Immunology, and Department of Immunology (V.A.S.H.D.), Erasmus University Medical Center, Rotterdam, the Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases (A.G., H.M.G.G.), and the Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam (N.A.K.), Amsterdam, the Department of Internal Medicine and Infectious Diseases (D.F.P.), and the Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen (A.L.W.H., D.B.), Groningen, the Department of Infectious Diseases, Leiden University Medical Center, Leiden (L.G.V.), and the Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven (D.B.) - all in the Netherlands
| | - Rory D de Vries
- From the Departments of Internal Medicine (R.S.G.S., M.L.), Hospital Pharmacy (R.S.G.S., W.J.R.R., P.H.M.K.), and Viroscience (D.G., K.S.S., M.P.G.K., C.H.G., R.D.V.) and the Department of Internal Medicine, Division of Allergy and Clinical Immunology, and Department of Immunology (V.A.S.H.D.), Erasmus University Medical Center, Rotterdam, the Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases (A.G., H.M.G.G.), and the Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam (N.A.K.), Amsterdam, the Department of Internal Medicine and Infectious Diseases (D.F.P.), and the Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen (A.L.W.H., D.B.), Groningen, the Department of Infectious Diseases, Leiden University Medical Center, Leiden (L.G.V.), and the Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven (D.B.) - all in the Netherlands
| | - P Hugo M van der Kuy
- From the Departments of Internal Medicine (R.S.G.S., M.L.), Hospital Pharmacy (R.S.G.S., W.J.R.R., P.H.M.K.), and Viroscience (D.G., K.S.S., M.P.G.K., C.H.G., R.D.V.) and the Department of Internal Medicine, Division of Allergy and Clinical Immunology, and Department of Immunology (V.A.S.H.D.), Erasmus University Medical Center, Rotterdam, the Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases (A.G., H.M.G.G.), and the Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam (N.A.K.), Amsterdam, the Department of Internal Medicine and Infectious Diseases (D.F.P.), and the Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen (A.L.W.H., D.B.), Groningen, the Department of Infectious Diseases, Leiden University Medical Center, Leiden (L.G.V.), and the Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven (D.B.) - all in the Netherlands
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van Kampen JJA, Dalm VASH, Fraaij PLA, Oude Munnink BB, Schapendonk CME, Izquierdo-Lara RW, Villabruna N, Ettayebi K, Estes MK, Koopmans MPG, de Graaf M. Clinical and In Vitro Evidence Favoring Immunoglobulin Treatment of a Chronic Norovirus Infection in a Patient With Common Variable Immunodeficiency. J Infect Dis 2022; 226:1781-1789. [PMID: 35255136 PMCID: PMC9650502 DOI: 10.1093/infdis/jiac085] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 10/22/2021] [Accepted: 03/04/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Immunocompromised individuals can become chronically infected with norovirus, but effective antiviral therapies are not yet available. METHODS Treatments with nitazoxanide, ribavirin, interferon alpha-2a, and nasoduodenally administered immunoglobulins were evaluated sequentially in an immunocompromised patient chronically infected with norovirus. In support, these components were also applied to measure norovirus inhibition in intestinal enteroid cultures in vitro. Viral RNA levels were determined in fecal and plasma samples during each treatment and viral genomes were sequenced. RESULTS None of the antivirals resulted in a reduction of viral RNA levels in feces or plasma. However, during ribavirin treatment, there was an increased accumulation of virus genome mutations. In vitro, an effect of interferon alpha-2a on virus replication was observed and a genetically related strain was neutralized effectively in vitro using immunoglobulins and post-norovirus-infection antiserum. In agreement, after administration of immunoglobulins, the patient cleared the infection. CONCLUSIONS Intestinal enteroid cultures provide a relevant system to evaluate antivirals and the neutralizing potential of immunoglobulins. We successfully treated a chronically infected patient with immunoglobulins, despite varying results reported by others. This case study provides in-depth, multifaceted exploration of norovirus treatment that can be used as a guidance for further research towards norovirus treatments.
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Affiliation(s)
| | | | - Pieter L A Fraaij
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Ray W Izquierdo-Lara
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Nele Villabruna
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Khalil Ettayebi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA,Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Miranda de Graaf
- Correspondence: Miranda de Graaf, PhD, Erasmus University Medical Center, PO Box 1738, 3000 DR Rotterdam, the Netherlands ()
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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 Vries-Sluijs TEMS, Bax HI, van Gorp ECM, de Jong-Peltenburg NC, de Mendonç A Melo M, van Nood E, Nouwen JL, Rijnders BJA, Rokx C, Schurink CAM, Slobbe L, Verbon A, Bassant N, van Beek JEA, Vriesde M, van Zonneveld LM, de Groot J, Boucher CAB, Koopmans MPG, van Kampen JJA, Fraaij PLA, van Rossum AMC, Vermont CL, van der Knaap LC, Visser E, Branger J, Douma RA, Cents-Bosma AS, Duijf-van de Ven CJHM, Schippers EF, van Nieuwkoop C, van Ijperen JM, Geilings J, van der Hut G, van Burgel ND, Leyten EMS, Gelinck LBS, Mollema F, Davids-Veldhuis S, Tearno C, Wildenbeest GS, Heikens E, Groeneveld PHP, Bouwhuis JW, Lammers AJJ, Kraan S, van Hulzen AGW, Kruiper MSM, van der Bliek GL, Bor PCJ, Debast SB, Wagenvoort GHJ, Kroon FP, de Boer MGJ, Jolink H, Lambregts MMC, Roukens AHE, Scheper H, Dorama W, van Holten N, Claas ECJ, Wessels E, den Hollander JG, El Moussaoui R, Pogany K, Brouwer CJ, Smit JV, Struik-Kalkman D, van Niekerk T, Pontesilli O, Lowe SH, Oude Lashof AML, Posthouwer D, van Wolfswinkel ME, Ackens RP, Burgers K, Schippers J, Weijenberg-Maes B, van Loo IHM, Havenith TRA, van Vonderen MGA, Kampschreur LM, Faber S, Steeman-Bouma R, Al Moujahid A, Kootstra GJ, Delsing CE, van der Burg-van de Plas M, Scheiberlich L, Kortmann W, van Twillert G, Renckens R, Ruiter-Pronk D, van Truijen-Oud FA, Cohen Stuart JWT, Jansen ER, Hoogewerf M, Rozemeijer W, van der Reijden WA, Sinnige JC, Brinkman K, van den Berk GEL, Blok WL, Lettinga KD, de Regt M, Schouten WEM, Stalenhoef JE, Veenstra J, Vrouenraets SME, Blaauw H, Geerders GF, Kleene MJ, Kok M, Knapen M, van der Meché IB, Mulder-Seeleman E, Toonen AJM, Wijnands S, Wttewaal E, Kwa D, van Crevel R, van Aerde K, Dofferhoff ASM, Henriet SSV, Ter Hofstede HJM, Hoogerwerf J, Keuter M, Richel O, Albers M, Grintjes-Huisman KJT, de Haan M, Marneef M, Strik-Albers R, Rahamat-Langendoen J, Stelma FF, Burger D, Gisolf EH, Hassing RJ, Claassen M, Ter Beest G, van Bentum PHM, Langebeek N, Tiemessen R, Swanink CMA, van Lelyveld SFL, Soetekouw R, van der Prijt LMM, van der Swaluw J, Bermon N, van der Reijden WA, Jansen R, Herpers BL, Veenendaal D, Verhagen DWM, Lauw FN, van Broekhuizen MC, van Wijk M, Bierman WFW, Bakker M, Kleinnijenhuis J, Kloeze E, Middel A, Postma DF, Schölvinck EH, Stienstra Y, Verhage AR, Wouthuyzen-Bakker M, Boonstra A, de Groot-de Jonge H, van der Meulen PA, de Weerd DA, Niesters HGM, van Leer-Buter CC, Knoester M, Hoepelman AIM, Arends JE, Barth RE, Bruns AHW, Ellerbroek PM, Mudrikova T, Oosterheert JJ, Schadd EM, van Welzen BJ, Aarsman K, Griffioen-van Santen BMG, de Kroon I, van Berkel M, van Rooijen CSAM, Schuurman R, Verduyn-Lunel F, Wensing AMJ, Bont LJ, Geelen SPM, Loeffen YGT, Wolfs TFW, Nauta N, Rooijakkers EOW, Holtsema H, Voigt R, van de Wetering D, Alberto A, van der Meer I, Rosingh A, Halaby T, Zaheri S, Boyd AC, Bezemer DO, van Sighem AI, Smit C, Hillebregt M, de Jong A, Woudstra T, Bergsma D, Meijering R, van de Sande L, Rutkens T, van der Vliet S, de Groot L, van den Akker 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, Raymond I, Viallard JF, Chaigne de Lalande S, Garipuy D, Delobel P, Obadia M, Cuzin L, Alvarez M, Biezunski N, Porte L, Massip P, Debard A, Balsarin F, Lagarrigue M, Prevoteau du Clary F, Aquilina C, Reynes J, Baillat V, Merle C, Lemoing V, Atoui N, Makinson A, Jacquet JM, Psomas C, Tramoni C, Aumaitre H, Saada M, Medus M, Malet M, Eden A, Neuville S, Ferreyra M, Sotto A, Barbuat C, Rouanet I, Leureillard D, Mauboussin JM, Lechiche C, Donsesco R, Cabie A, Abel S, Pierre-Francois S, Batala AS, Cerland C, Rangom C, Theresine N, Hoen B, Lamaury I, Fabre I, Schepers K, Curlier E, Ouissa R, Gaud C, Ricaud C, Rodet R, Wartel G, Sautron C, Beck-Wirth G, Michel C, Beck C, Halna JM, Kowalczyk J, Benomar M, Drobacheff-Thiebaut C, Chirouze C, Faucher JF, Parcelier F, Foltzer A, Haffner-Mauvais C, Hustache Mathieu M, Proust A, Piroth L, Chavanet P, Duong M, Buisson M, Waldner A, Mahy S, Gohier S, Croisier D, May T, Delestan M, Andre M, Zadeh MM, Martinot M, Rosolen B, Pachart A, Martha B, Jeunet 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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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