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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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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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3
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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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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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