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Geubbels ELPE, Backer JA, Bakhshi-Raiez F, van der Beek RFHJ, van Benthem BHB, van den Boogaard J, Broekman EH, Dongelmans DA, Eggink D, van Gaalen RD, van Gageldonk A, Hahné S, Hajji K, Hofhuis A, van Hoek AJ, Kooijman MN, Kroneman A, Lodder W, van Rooijen M, Roorda W, Smorenburg N, Zwagemaker F, de Keizer NF, van Walle I, de Roda Husman AM, Ruijs C, van den Hof S. The daily updated Dutch national database on COVID-19 epidemiology, vaccination and sewage surveillance. Sci Data 2023; 10:469. [PMID: 37474530 PMCID: PMC10359398 DOI: 10.1038/s41597-023-02232-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 05/12/2023] [Indexed: 07/22/2023] Open
Abstract
The Dutch national open database on COVID-19 has been incrementally expanded since its start on 30 April 2020 and now includes datasets on symptoms, tests performed, individual-level positive cases and deaths, cases and deaths among vulnerable populations, settings of transmission, hospital and ICU admissions, SARS-CoV-2 variants, viral loads in sewage, vaccinations and the effective reproduction number. This data is collected by municipal health services, laboratories, hospitals, sewage treatment plants, vaccination providers and citizens and is cleaned, analysed and published, mostly daily, by the National Institute for Public Health and the Environment (RIVM) in the Netherlands, using automated scripts. Because these datasets cover the key aspects of the pandemic and are available at detailed geographical level, they are essential to gain a thorough understanding of the past and current COVID-19 epidemiology in the Netherlands. Future purposes of these datasets include country-level comparative analysis on the effect of non-pharmaceutical interventions against COVID-19 in different contexts, such as different cultural values or levels of socio-economic disparity, and studies on COVID-19 and weather factors.
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Affiliation(s)
- E L P E Geubbels
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands.
| | - J A Backer
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - F Bakhshi-Raiez
- National Intensive Care Evaluation (NICE) foundation, Amsterdam, the Netherlands
| | - R F H J van der Beek
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - B H B van Benthem
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - J van den Boogaard
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- The network of regional epidemiological consultants (REC), Bilthoven, the Netherlands
| | | | - D A Dongelmans
- National Intensive Care Evaluation (NICE) foundation, Amsterdam, the Netherlands
- Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - D Eggink
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - R D van Gaalen
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - A van Gageldonk
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - S Hahné
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - K Hajji
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - A Hofhuis
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - A J van Hoek
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - M N Kooijman
- Centre of Information Services and CIO office, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - A Kroneman
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - W Lodder
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - M van Rooijen
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - W Roorda
- GGD GHOR Nederland, Utrecht, the Netherlands
| | - N Smorenburg
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - F Zwagemaker
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - N F de Keizer
- National Intensive Care Evaluation (NICE) foundation, Amsterdam, the Netherlands
- Department of Medical Informatics, Amsterdam UMC, Amsterdam Public Health research institute, University of Amsterdam, Amsterdam, the Netherlands
| | - I van Walle
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - A M de Roda Husman
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - C Ruijs
- GGD GHOR Nederland, Utrecht, the Netherlands
| | - S van den Hof
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands.
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Kolodziej LM, van Lelyveld SFL, Haverkort ME, Mariman R, Sluiter-Post JGC, Badoux P, de Koff EM, Koole JCD, Miellet WR, Swart AN, Coipan EC, Meijer A, Sanders EAM, Trzciński K, Euser SM, Eggink D, van Houten MA. High SARS-CoV-2 household transmission rates detected by dense saliva sampling. Clin Infect Dis 2022; 75:e10-e19. [PMID: 35385575 PMCID: PMC9047155 DOI: 10.1093/cid/ciac261] [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: 01/14/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Understanding the dynamics of SARS-CoV-2 household transmission is important for adequate infection control measures in this ongoing pandemic. METHODS Households were enrolled upon a PCR-confirmed index case between October and December 2020, prior to the COVID-19 vaccination program. Saliva samples were obtained by self-sampling at day 1, 3, 5, 7, 10, 14, 21, 28, 35, and 42 from study inclusion. Nasopharyngeal swabs (NPS) and oropharyngeal swabs (OPS) were collected by the research team at day 7 and capillary blood samples at day 42. Household secondary attack rate (SAR) and per-person SAR were calculated based on at least one positive saliva, NPS, OPS, or serum sample. Whole genome sequencing was performed to investigate the possibility of multiple independent SARS-CoV-2 introductions within a household. RESULTS Eighty-five households were included consisting of 326 (unvaccinated) individuals. Comparable numbers of secondary cases were identified by saliva (133/241; 55.2%) and serum (127/213; 59.6%). The household SAR was 88.2%. The per-person SAR was 64.3%. The majority of the secondary cases tested positive in saliva at day 1 (103/150; 68.7%). Transmission from index case to household member was not affected by age or the nature of their relationship. Phylogenetic analyses suggested a single introduction for the investigated households. CONCLUSION Households have a pivotal role in SARS-CoV-2 transmission. By repeated saliva self-sampling combined with NPS, OPS, and serology, we found the highest SARS-CoV-2 household transmission rates reported to date. Salivary (self-)sampling of adults and children is suitable and attractive for near real-time monitoring of SARS-CoV-2 transmission in this setting.
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Affiliation(s)
- L M Kolodziej
- Spaarne Gasthuis Academy, Hoofddorp, The Netherlands
| | - S F L van Lelyveld
- Department of Internal Medicine, Spaarne Gasthuis Hospital, Haarlem/Hoofddorp, The Netherlands
| | - M E Haverkort
- Public Health Services Kennemerland, Haarlem, The Netherlands
| | - R Mariman
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | | | - P Badoux
- Spaarne Gasthuis Academy, Hoofddorp, The Netherlands
| | - E M de Koff
- Spaarne Gasthuis Academy, Hoofddorp, The Netherlands
| | - J C D Koole
- Spaarne Gasthuis Academy, Hoofddorp, The Netherlands.,(current affiliation) Public Health Services Amsterdam, Amsterdam, The Netherlands
| | - W R Miellet
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands.,Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, The Netherlands
| | - A N Swart
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - E C Coipan
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - A Meijer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - E A M Sanders
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - K Trzciński
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, The Netherlands
| | - S M Euser
- Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - D Eggink
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - M A van Houten
- Spaarne Gasthuis Academy, Hoofddorp, The Netherlands.,Department of Paediatrics, Spaarne Gasthuis, Haarlem/Hoofddorp, The Netherlands
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Koel BF, Vigeveno RM, Pater M, Koekkoek SM, Han AX, Tuan HM, Anh TTN, Hung NT, Thinh LQ, Hai LT, Ngoc HTB, Chau NVV, Ngoc NM, Chokephaibulkit K, Puthavathana P, Kinh NV, Trinh T, Lee RTC, Maurer-Stroh S, Eggink D, Thanh TT, Tan LV, van Doorn HR, de Jong MD. Longitudinal sampling is required to maximize detection of intrahost A/H3N2 virus variants. Virus Evol 2020; 6:veaa088. [PMID: 33343927 PMCID: PMC7733607 DOI: 10.1093/ve/veaa088] [Citation(s) in RCA: 2] [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: 12/20/2022] Open
Abstract
Seasonal human influenza viruses continually change antigenically to escape from neutralizing antibodies. It remains unclear how genetic variation in the intrahost virus population and selection at the level of individual hosts translates to the fast-paced evolution observed at the global level because emerging intrahost antigenic variants are rarely detected. We tracked intrahost variants in the hemagglutinin and neuraminidase surface proteins using longitudinally collected samples from 52 patients infected by A/H3N2 influenza virus, mostly young children, who received oseltamivir treatment. We identified emerging putative antigenic variants and oseltamivir-resistant variants, most of which remained detectable in samples collected at subsequent days, and identified variants that emerged intrahost immediately prior to increases in global rates. In contrast to most putative antigenic variants, oseltamivir-resistant variants rapidly increased to high frequencies in the virus population. Importantly, the majority of putative antigenic variants and oseltamivir-resistant variants were first detectable four or more days after onset of symptoms or start of treatment, respectively. Our observations demonstrate that de novo variants emerge, and may be positively selected, during the course of infection. Additionally, based on the 4–7 days post-treatment delay in emergence of oseltamivir-resistant variants in six out of the eight individuals with such variants, we find that limiting sample collection for routine surveillance and diagnostic testing to early timepoints after onset of symptoms can potentially preclude detection of emerging, positively selected variants.
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Affiliation(s)
- B F Koel
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - R M Vigeveno
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - M Pater
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - S M Koekkoek
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - A X Han
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | | | | | - N T Hung
- Children's Hospital 1, Ho Chi Minh City, Vietnam
| | - L Q Thinh
- Children's Hospital 1, Ho Chi Minh City, Vietnam
| | - L T Hai
- Vietnam National Children's Hospital, Hanoi, Vietnam
| | - H T B Ngoc
- Vietnam National Children's Hospital, Hanoi, Vietnam
| | - N V V Chau
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - N M Ngoc
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | | | | | - N V Kinh
- National Hospital of Tropical Diseases, Hanoi, Vietnam
| | - T Trinh
- National Hospital of Tropical Diseases, Hanoi, Vietnam
| | - R T C Lee
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore 138671 Singapore
| | - S Maurer-Stroh
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore 138671 Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore.,National Public Health Laboratory, National Centre for Infectious Diseases, Ministry of Health, Singapore 308442, Singapore
| | - D Eggink
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - T T Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - L V Tan
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - H R van Doorn
- Oxford University Clinical Research Unit, Hanoi, Vietnam.,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - M D de Jong
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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Melchers M, Bontjer I, Tong T, Chung N, Klasse P, Eggink D, Gentile M, Cerutti A, Montefiori D, Olson W, Berkhout B, Binley J, Moore J, Sanders R. Targeting HIV-1 envelope glycoprotein trimers to B cells using APRIL improves antibody responses. Retrovirology 2012. [PMCID: PMC3441255 DOI: 10.1186/1742-4690-9-s2-p300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
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5
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Melchers M, Matthews K, van Montfort T, Bontjer I, Eggink D, de Vries R, Michael E, David K, Moore JP, Berkhout B, Sanders RW. P05-05. Enhanced immunogenicity of HIV-1 envelope glycoprotein trimers fused to CD40 ligand. Retrovirology 2009. [PMCID: PMC2767986 DOI: 10.1186/1742-4690-6-s3-p81] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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