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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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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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Andeweg SP, Vennema H, Veldhuijzen I, Smorenburg N, Schmitz D, Zwagemaker F, van Gageldonk-Lafeber AB, Hahné SJM, Reusken C, Knol MJ, Eggink D. Elevated risk of infection with SARS-CoV-2 Beta, Gamma, and Delta variants compared with Alpha variant in vaccinated individuals. Sci Transl Med 2023; 15:eabn4338. [PMID: 35862508 PMCID: PMC9580257 DOI: 10.1126/scitranslmed.abn4338] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 07/08/2022] [Indexed: 12/22/2022]
Abstract
The extent to which severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) break through infection- or vaccine-induced immunity is not well understood. We analyzed 28,578 sequenced SARS-CoV-2 samples from individuals with known immune status obtained through national community testing in the Netherlands from March to August 2021. We found evidence of an increased risk of infection by the Beta (B.1.351), Gamma (P.1), or Delta (B.1.617.2) variants compared with the Alpha (B.1.1.7) variant after vaccination. No clear differences were found between vaccines. However, the effect was larger in the first 14 to 59 days after complete vaccination compared with ≥60 days. In contrast to vaccine-induced immunity, there was no increased risk for reinfection with Beta, Gamma, or Delta variants relative to the Alpha variant in individuals with infection-induced immunity.
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Affiliation(s)
- Stijn P. Andeweg
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3720 BA, Bilthoven, Netherlands
| | - Harry Vennema
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3720 BA, Bilthoven, Netherlands
| | - Irene Veldhuijzen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3720 BA, Bilthoven, Netherlands
| | - Naomi Smorenburg
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3720 BA, Bilthoven, Netherlands
| | - Dennis Schmitz
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3720 BA, Bilthoven, Netherlands
| | - Florian Zwagemaker
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3720 BA, Bilthoven, Netherlands
| | - Arianne B. van Gageldonk-Lafeber
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3720 BA, Bilthoven, Netherlands
| | - Susan J. M. Hahné
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3720 BA, Bilthoven, Netherlands
| | - Chantal Reusken
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3720 BA, Bilthoven, Netherlands
| | - Mirjam J. Knol
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3720 BA, Bilthoven, Netherlands
| | - Dirk Eggink
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3720 BA, Bilthoven, Netherlands
| | - SeqNeth Molecular surveillance group†
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3720 BA, Bilthoven, Netherlands
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