1
|
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.
Collapse
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.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
van Beek J, Teesing G, Oude Munnink BB, Meima A, Vriend HJ, Elzakkers J, de Graaf M, Langeveld J, Medema GJ, Molenkamp R, Voeten H, Fanoy E, Koopmans M. Population-based screening in a municipality after a primary school outbreak of the SARS-CoV-2 Alpha variant, the Netherlands, December 2020-February 2021. PLoS One 2022; 17:e0276696. [PMID: 36301829 PMCID: PMC9612486 DOI: 10.1371/journal.pone.0276696] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 10/11/2022] [Indexed: 11/18/2022] Open
Abstract
An outbreak of SARS-CoV-2 Alpha variant (Pango lineage B.1.1.7) was detected at a primary school (School X) in Lansingerland, the Netherlands, in December 2020. The outbreak was studied retrospectively, and population-based screening was used to assess the extent of virus circulation and decelerate transmission. Cases were SARS-CoV-2 laboratory confirmed and were residents of Lansingerland (November 16th 2020 until February 22th 2021), or had an epidemiological link with School X or neighbouring schools. The SARS-CoV-2 variant was determined using variant PCR or whole genome sequencing. A questionnaire primarily assessed clinical symptoms. A total of 77 Alpha variant cases were found with an epidemiological link to School X, 16 Alpha variant cases linked to the neighbouring schools, and 146 Alpha variant cases among residents of Lansingerland without a link to the schools. The mean number of self-reported symptoms was not significantly different among Alpha variant infected individuals compared to non-Alpha infected individuals. The secondary attack rate (SAR) among Alpha variant exposed individuals in households was 52% higher compared to non-Alpha variant exposed individuals (p = 0.010), with the mean household age, and mean number of children and adults per household as confounders. Sequence analysis of 60 Alpha variant sequences obtained from cases confirmed virus transmission between School X and neighbouring schools, and showed that multiple introductions of the Alpha variant had already taken place in Lansingerland at the time of the study. The alpha variant caused a large outbreak at both locations of School X, and subsequently spread to neighbouring schools, and households. Population-based screening (together with other public health measures) nearly stopped transmission of the outbreak strain, but did not prevent variant replacement in the Lansingerland municipality.
Collapse
Affiliation(s)
- Janko van Beek
- Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- * E-mail:
| | - Gwen Teesing
- Department of Infectious Disease Control, Public Health Service Rotterdam-Rijnmond, Rotterdam, The Netherlands
- The Netherlands Organization for Health Research and Development (ZonMw), The Hague, The Netherlands
| | - Bas B. Oude Munnink
- Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Abraham Meima
- Department of Infectious Disease Control, Public Health Service Rotterdam-Rijnmond, Rotterdam, The Netherlands
| | - Henrike J. Vriend
- Department of Infectious Disease Control, Public Health Service Rotterdam-Rijnmond, Rotterdam, The Netherlands
| | - Jessica Elzakkers
- Department of Infectious Disease Control, Public Health Service Rotterdam-Rijnmond, Rotterdam, The Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jeroen Langeveld
- KWR Water Research Institute, Nieuwegein, The Netherlands
- Partners4UrbanWater, Nijmegen, The Netherlands
| | - Gert-Jan Medema
- KWR Water Research Institute, Nieuwegein, The Netherlands
- Sanitary Engineering, Delft University of Technology, Delft, The Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Helene Voeten
- Department of Infectious Disease Control, Public Health Service Rotterdam-Rijnmond, Rotterdam, The Netherlands
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ewout Fanoy
- Department of Infectious Disease Control, Public Health Service Rotterdam-Rijnmond, Rotterdam, The Netherlands
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | |
Collapse
|
6
|
Vink M, Iglói Z, Fanoy EB, van Beek J, Boelsums T, de Graaf M, Voeten HACM, Molenkamp R, Koopmans MP, Mevissen FE. Community-based SARS-CoV-2 testing in low-income neighbourhoods in Rotterdam: Results from a pilot study. J Glob Health 2022; 12:05042. [PMID: 36181719 PMCID: PMC9526478 DOI: 10.7189/jogh.12.05042] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background High incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and low testing uptake were reported in low-income neighbourhoods in Rotterdam. We aimed to improve willingness and access to testing by introducing community-based test facilities, and to evaluate the effectiveness of a rapid antigen detection test (RDT). Methods Two to eleven test facilities operated consecutively in three low-income neighbourhoods in Rotterdam, offering the options of walk-in or appointments. Background characteristics were collected at intake and one nasopharyngeal swab was taken and processed using both RDT and reverse transcription polymerase chain reaction (RT-PCR). Visitors were asked to join a survey for evaluation purposes. Results In total, 19 773 visitors were tested - 9662 (48.9%) without an appointment. Walk-in visitors were older, lived more often in the proximity of the test facilities, and reported coronavirus disease (COVID-19)-related symptoms less often than by-appointment visitors. For 67.7% of the visitors, this was the first time they got tested. A total of 1211 (6.1%) tested SARS-CoV-2-positive with RT-PCR, of whom 309 (25.5%) were asymptomatic. Test uptake increased among residents of the pilot neighbourhoods, especially in the older age groups, compared to people living in comparable neighbourhoods without community-based testing facilities. RDT detected asymptomatic individuals with 71.8% sensitivity, which was acceptable in this high prevalence setting. Visitors reported positive attitudes towards the test facilities and welcomed the easy access. Conclusions Offering community-based SARS-CoV-2 testing seems a promising approach for increasing testing uptake among specific populations in low-income neighbourhoods.
Collapse
Affiliation(s)
- Martijn Vink
- Public Health Service (GGD) Rotterdam-Rijnmond, Rotterdam, the Netherlands
| | - Zsófia Iglói
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Ewout B Fanoy
- Public Health Service (GGD) Rotterdam-Rijnmond, Rotterdam, the Netherlands
| | - Janko van Beek
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Timo Boelsums
- Public Health Service (GGD) Rotterdam-Rijnmond, Rotterdam, the Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | | | | | | | | |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Agrawal S, Orschler L, Schubert S, Zachmann K, Heijnen L, Tavazzi S, Gawlik BM, de Graaf M, Medema G, Lackner S. Prevalence and circulation patterns of SARS-CoV-2 variants in European sewage mirror clinical data of 54 European cities. Water Res 2022; 214:118162. [PMID: 35193077 PMCID: PMC8817224 DOI: 10.1016/j.watres.2022.118162] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/28/2022] [Accepted: 02/03/2022] [Indexed: 05/04/2023]
Abstract
For community-level monitoring, the European Commission under the EU Sewage Sentinel System recommends wastewater-based SARS-CoV-2 surveillance. Tracking SARS-CoV-2 variants in a community is pivotal for appropriate public health response. Genome sequencing of SARS-CoV-2 in wastewater samples for tracking variants is challenging, often resulting in low coverage genome sequences, thereby impeding the detection of the SARS-CoV-2 mutations. Therefore, we aimed at high-coverage SARS-CoV-2 genome sequences from sewage samples which we successfully accomplished. This first pan-European surveillance compared the mutation profiles associated with the variants of concerns: B.1.1.7, P.1, B.1.351 and B.1.617.2 across 20 European countries, including 54 municipalities. The results highlight that SARS-CoV-2 variants detected in the wastewater samples mirror the variants profiles reported in clinical data. This study demonstrated that >98% coverage of SARS-CoV-2 genomic sequences is possible and can be used to track SARS-CoV-2 mutations in wastewater to support identifying variants circulating in a city at the community level.
Collapse
Affiliation(s)
- Shelesh Agrawal
- Department of Civil and Environmental Engineering Sciences, Institute IWAR, Chair of Water and Environmental Biotechnology, Technical University of Darmstadt, Darmstadt, Germany.
| | - Laura Orschler
- Department of Civil and Environmental Engineering Sciences, Institute IWAR, Chair of Water and Environmental Biotechnology, Technical University of Darmstadt, Darmstadt, Germany
| | - Selina Schubert
- Department of Civil and Environmental Engineering Sciences, Institute IWAR, Chair of Water and Environmental Biotechnology, Technical University of Darmstadt, Darmstadt, Germany
| | - Kira Zachmann
- Department of Civil and Environmental Engineering Sciences, Institute IWAR, Chair of Water and Environmental Biotechnology, Technical University of Darmstadt, Darmstadt, Germany
| | - Leo Heijnen
- KWR Water Research Institute, Nieuwegein, the Netherland
| | - Simona Tavazzi
- European Commission, Joint Research Centre, Ispra, VA, Italy
| | | | - Miranda de Graaf
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherland
| | - Gertjan Medema
- KWR Water Research Institute, Nieuwegein, the Netherland
| | - Susanne Lackner
- Department of Civil and Environmental Engineering Sciences, Institute IWAR, Chair of Water and Environmental Biotechnology, Technical University of Darmstadt, Darmstadt, Germany
| |
Collapse
|
9
|
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.
Collapse
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 ()
| |
Collapse
|
10
|
Heijnen L, Elsinga G, de Graaf M, Molenkamp R, Koopmans MPG, Medema G. Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. Sci Total Environ 2021; 799:149456. [PMID: 34371414 PMCID: PMC8332926 DOI: 10.1016/j.scitotenv.2021.149456] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [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: 03/30/2021] [Revised: 06/15/2021] [Accepted: 07/31/2021] [Indexed: 04/15/2023]
Abstract
Wastewater surveillance has shown to be a valuable and efficient tool to obtain information about the trends of COVID-19 in the community. Since the recent emergence of new variants, associated with increased transmissibility and/or antibody escape (variants of concern), there is an urgent need for methods that enable specific and timely detection and quantification of the occurrence of these variants in the community. In this study, we demonstrate the use of RT-ddPCR on wastewater samples for specific detection of mutation N501Y. This assay enabled simultaneous enumeration of lineage B.1.351 (containing the 501Y mutation) and Wild Type (WT, containing 501N) SARS-CoV-2 RNA. Detection of N501Y was possible in samples with mixtures of WT with low proportions of B.1.351 (0.5%) and could accurately determine the proportion of N501Y and WT in mixtures of SARS-CoV-2 RNA. The application to raw sewage samples from the cities of Amsterdam and Utrecht demonstrated that this method can be applied to wastewater samples. The emergence of N501Y in Amsterdam and Utrecht wastewater aligned with the emergence of B.1.1.7 as causative agent of COVID-19 in the Netherlands, indicating that RT-ddPCR of wastewater samples can be used to monitor the emergence of the N501Y mutation in the community. It also indicates that RT-ddPCR could be used for sensitive and accurate monitoring of current (like K417N, K417T, E484K, L452R) or future mutations present in SARS-CoV-2 variants of concern. Monitoring these mutations can be used to obtain insight in the introduction and spread of VOC and support public health decision-making regarding measures to limit viral spread or allocation of testing or vaccination.
Collapse
Affiliation(s)
- Leo Heijnen
- KWR Water Research Institute, Nieuwegein, the Netherlands.
| | - Goffe Elsinga
- KWR Water Research Institute, Nieuwegein, the Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Gertjan Medema
- KWR Water Research Institute, Nieuwegein, the Netherlands
| |
Collapse
|
11
|
Heijnen L, Elsinga G, de Graaf M, Molenkamp R, Koopmans MPG, Medema G. Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. Sci Total Environ 2021; 799:149456. [PMID: 34371414 DOI: 10.1101/2021.03.25.21254324] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 03/30/2021] [Revised: 06/15/2021] [Accepted: 07/31/2021] [Indexed: 05/20/2023]
Abstract
Wastewater surveillance has shown to be a valuable and efficient tool to obtain information about the trends of COVID-19 in the community. Since the recent emergence of new variants, associated with increased transmissibility and/or antibody escape (variants of concern), there is an urgent need for methods that enable specific and timely detection and quantification of the occurrence of these variants in the community. In this study, we demonstrate the use of RT-ddPCR on wastewater samples for specific detection of mutation N501Y. This assay enabled simultaneous enumeration of lineage B.1.351 (containing the 501Y mutation) and Wild Type (WT, containing 501N) SARS-CoV-2 RNA. Detection of N501Y was possible in samples with mixtures of WT with low proportions of B.1.351 (0.5%) and could accurately determine the proportion of N501Y and WT in mixtures of SARS-CoV-2 RNA. The application to raw sewage samples from the cities of Amsterdam and Utrecht demonstrated that this method can be applied to wastewater samples. The emergence of N501Y in Amsterdam and Utrecht wastewater aligned with the emergence of B.1.1.7 as causative agent of COVID-19 in the Netherlands, indicating that RT-ddPCR of wastewater samples can be used to monitor the emergence of the N501Y mutation in the community. It also indicates that RT-ddPCR could be used for sensitive and accurate monitoring of current (like K417N, K417T, E484K, L452R) or future mutations present in SARS-CoV-2 variants of concern. Monitoring these mutations can be used to obtain insight in the introduction and spread of VOC and support public health decision-making regarding measures to limit viral spread or allocation of testing or vaccination.
Collapse
Affiliation(s)
- Leo Heijnen
- KWR Water Research Institute, Nieuwegein, the Netherlands.
| | - Goffe Elsinga
- KWR Water Research Institute, Nieuwegein, the Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Gertjan Medema
- KWR Water Research Institute, Nieuwegein, the Netherlands
| |
Collapse
|
12
|
van Loben Sels JM, Meredith LW, Sosnovtsev SV, de Graaf M, Koopmans MP, Lindesmith LC, Baric RS, Green KY, Goodfellow IG. A luciferase-based approach for measuring HBGA blockade antibody titers against human norovirus. J Virol Methods 2021; 297:114196. [PMID: 34019938 PMCID: PMC9924141 DOI: 10.1016/j.jviromet.2021.114196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 05/13/2021] [Accepted: 05/17/2021] [Indexed: 01/14/2023]
Abstract
BACKGROUND Noroviruses are the most common cause of viral gastroenteritis worldwide, yet there is a deficit in the understanding of protective immunity. Surrogate neutralization assays have been widely used that measure the ability of antibodies to block virus-like particle (VLP) binding to histo-blood group antigens (HBGAs). However, screening large sample sets against multiple antigens using the traditional HBGA blocking assay requires significant investment in terms of time, equipment, and technical expertise, largely associated with the generation of purified VLPs. METHODS To address these issues, a luciferase immunoprecipitation system (LIPS) assay was modified to measure the norovirus-specific HBGA blockade activity of antibodies. The assay (designated LIPS-Blockade) was validated using a panel of well-characterized homotypic and heterotypic hyperimmune sera as well as strain-specific HBGA blocking monoclonal antibodies. RESULTS The LIPS-Blockade assay was comparable in specificity to a standard HBGA blocking protocol performed with VLPs. Using time-ordered patient sera, the luciferase-based approach was also able to detect changes in HBGA blocking titers following viral challenge and natural infection with norovirus. CONCLUSION In this study we developed a rapid, robust, and scalable surrogate neutralization assay for noroviruses that circumvented the need for purified VLPs. This LIPS-Blockade assay should streamline the process of large-scale immunological studies, ultimately aiding in the characterization of protective immunity to human noroviruses.
Collapse
Affiliation(s)
- Jessica M. van Loben Sels
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, CB2 2QQ UK,Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, DHHS, Bethesda, MD, 20892 USA
| | - Luke W. Meredith
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, CB2 2QQ UK
| | - Stanislav V. Sosnovtsev
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, DHHS, Bethesda, MD, 20892 USA
| | - Miranda de Graaf
- Department of Viroscience, Erasmus University Medical Center, 3015 CN, Rotterdam, the Netherlands.
| | - Marion P.G. Koopmans
- Department of Viroscience, Erasmus University Medical Center, 3015 CN Rotterdam, NL
| | - Lisa C. Lindesmith
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - Kim Y. Green
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, DHHS, Bethesda, MD, 20892 USA,Corresponding author at: Dr. Kim Y. Green, Caliciviruses Section, LID/DIR/NIAID, National Institutes of Health (NIH), Building 50, Room 6318, 50 South Drive, Bethesda, MD 20892 USA –
| | - Ian G. Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, CB2 2QQ UK
| |
Collapse
|
13
|
Chan MCW, Roy S, Bonifacio J, Zhang LY, Chhabra P, Chan JCM, Celma C, Igoy MA, Lau SL, Mohammad KN, Vinjé J, Vennema H, Breuer J, Koopmans M, de Graaf M. Detection of Norovirus Variant GII.4 Hong Kong in Asia and Europe, 2017-2019. Emerg Infect Dis 2021; 27:289-293. [PMID: 33350912 PMCID: PMC7774557 DOI: 10.3201/eid2701.203351] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We report a new norovirus GII.4 variant, GII.4 Hong Kong, with low-level circulation in 4 Eurasia countries since mid-2017. Amino acid substitutions in key residues on the virus capsid associated with the emergence of pandemic noroviruses suggest that GII.4 Hong Kong has the potential to become the next pandemic variant.
Collapse
|
14
|
Izquierdo-Lara R, Elsinga G, Heijnen L, Munnink BBO, Schapendonk CME, Nieuwenhuijse D, Kon M, Lu L, Aarestrup FM, Lycett S, Medema G, Koopmans MPG, de Graaf M. Monitoring SARS-CoV-2 Circulation and Diversity through Community Wastewater Sequencing, the Netherlands and Belgium. Emerg Infect Dis 2021. [PMID: 33900177 DOI: 10.1101/2020.09.21.20198838] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly become a major global health problem, and public health surveillance is crucial to monitor and prevent virus spread. Wastewater-based epidemiology has been proposed as an addition to disease-based surveillance because virus is shed in the feces of ≈40% of infected persons. We used next-generation sequencing of sewage samples to evaluate the diversity of SARS-CoV-2 at the community level in the Netherlands and Belgium. Phylogenetic analysis revealed the presence of the most prevalent clades (19A, 20A, and 20B) and clustering of sewage samples with clinical samples from the same region. We distinguished multiple clades within a single sewage sample by using low-frequency variant analysis. In addition, several novel mutations in the SARS-CoV-2 genome were detected. Our results illustrate how wastewater can be used to investigate the diversity of SARS-CoV-2 viruses circulating in a community and identify new outbreaks.
Collapse
|
15
|
Izquierdo-Lara R, Elsinga G, Heijnen L, Munnink BBO, Schapendonk CME, Nieuwenhuijse D, Kon M, Lu L, Aarestrup FM, Lycett S, Medema G, Koopmans MPG, de Graaf M. Monitoring SARS-CoV-2 Circulation and Diversity through Community Wastewater Sequencing, the Netherlands and Belgium. Emerg Infect Dis 2021; 27:1405-1415. [PMID: 33900177 DOI: 10.1101/2020.09.21.20198838v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly become a major global health problem, and public health surveillance is crucial to monitor and prevent virus spread. Wastewater-based epidemiology has been proposed as an addition to disease-based surveillance because virus is shed in the feces of ≈40% of infected persons. We used next-generation sequencing of sewage samples to evaluate the diversity of SARS-CoV-2 at the community level in the Netherlands and Belgium. Phylogenetic analysis revealed the presence of the most prevalent clades (19A, 20A, and 20B) and clustering of sewage samples with clinical samples from the same region. We distinguished multiple clades within a single sewage sample by using low-frequency variant analysis. In addition, several novel mutations in the SARS-CoV-2 genome were detected. Our results illustrate how wastewater can be used to investigate the diversity of SARS-CoV-2 viruses circulating in a community and identify new outbreaks.
Collapse
|
16
|
Izquierdo-Lara R, Elsinga G, Heijnen L, Munnink BBO, Schapendonk CM, Nieuwenhuijse D, Kon M, Lu L, Aarestrup FM, Lycett S, Medema G, Koopmans MP, de Graaf M. Monitoring SARS-CoV-2 Circulation and Diversity through Community Wastewater Sequencing, the Netherlands and Belgium. Emerg Infect Dis 2021; 27:1405-1415. [PMID: 33900177 PMCID: PMC8084483 DOI: 10.3201/eid2705.204410] [Citation(s) in RCA: 137] [Impact Index Per Article: 45.7] [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] [Indexed: 12/16/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly become a major global health problem, and public health surveillance is crucial to monitor and prevent virus spread. Wastewater-based epidemiology has been proposed as an addition to disease-based surveillance because virus is shed in the feces of ≈40% of infected persons. We used next-generation sequencing of sewage samples to evaluate the diversity of SARS-CoV-2 at the community level in the Netherlands and Belgium. Phylogenetic analysis revealed the presence of the most prevalent clades (19A, 20A, and 20B) and clustering of sewage samples with clinical samples from the same region. We distinguished multiple clades within a single sewage sample by using low-frequency variant analysis. In addition, several novel mutations in the SARS-CoV-2 genome were detected. Our results illustrate how wastewater can be used to investigate the diversity of SARS-CoV-2 viruses circulating in a community and identify new outbreaks.
Collapse
Affiliation(s)
- Ray Izquierdo-Lara
- Erasmus University Medical Center, Rotterdam, the Netherlands (R. Izquierdo-Lara, B.B. Oude Munnink, C.M.E. Schapendonk, D. Nieuwenhuijse, M. Kon, M.P.G. Koopmans, M. de Graaf)
- KWR Water Research Institute, Nieuwegein, the Netherlands (G. Elsinga, L. Heijnen, G. Medema)
- University of Edinburgh, Edinburgh, Scotland, UK (L. Lu, S. Lycett)
- Technical University of Denmark, Kongens Lyngby, Denmark (F.M. Aarestrup)
| | - Goffe Elsinga
- Erasmus University Medical Center, Rotterdam, the Netherlands (R. Izquierdo-Lara, B.B. Oude Munnink, C.M.E. Schapendonk, D. Nieuwenhuijse, M. Kon, M.P.G. Koopmans, M. de Graaf)
- KWR Water Research Institute, Nieuwegein, the Netherlands (G. Elsinga, L. Heijnen, G. Medema)
- University of Edinburgh, Edinburgh, Scotland, UK (L. Lu, S. Lycett)
- Technical University of Denmark, Kongens Lyngby, Denmark (F.M. Aarestrup)
| | - Leo Heijnen
- Erasmus University Medical Center, Rotterdam, the Netherlands (R. Izquierdo-Lara, B.B. Oude Munnink, C.M.E. Schapendonk, D. Nieuwenhuijse, M. Kon, M.P.G. Koopmans, M. de Graaf)
- KWR Water Research Institute, Nieuwegein, the Netherlands (G. Elsinga, L. Heijnen, G. Medema)
- University of Edinburgh, Edinburgh, Scotland, UK (L. Lu, S. Lycett)
- Technical University of Denmark, Kongens Lyngby, Denmark (F.M. Aarestrup)
| | - Bas B. Oude Munnink
- Erasmus University Medical Center, Rotterdam, the Netherlands (R. Izquierdo-Lara, B.B. Oude Munnink, C.M.E. Schapendonk, D. Nieuwenhuijse, M. Kon, M.P.G. Koopmans, M. de Graaf)
- KWR Water Research Institute, Nieuwegein, the Netherlands (G. Elsinga, L. Heijnen, G. Medema)
- University of Edinburgh, Edinburgh, Scotland, UK (L. Lu, S. Lycett)
- Technical University of Denmark, Kongens Lyngby, Denmark (F.M. Aarestrup)
| | - Claudia M.E. Schapendonk
- Erasmus University Medical Center, Rotterdam, the Netherlands (R. Izquierdo-Lara, B.B. Oude Munnink, C.M.E. Schapendonk, D. Nieuwenhuijse, M. Kon, M.P.G. Koopmans, M. de Graaf)
- KWR Water Research Institute, Nieuwegein, the Netherlands (G. Elsinga, L. Heijnen, G. Medema)
- University of Edinburgh, Edinburgh, Scotland, UK (L. Lu, S. Lycett)
- Technical University of Denmark, Kongens Lyngby, Denmark (F.M. Aarestrup)
| | - David Nieuwenhuijse
- Erasmus University Medical Center, Rotterdam, the Netherlands (R. Izquierdo-Lara, B.B. Oude Munnink, C.M.E. Schapendonk, D. Nieuwenhuijse, M. Kon, M.P.G. Koopmans, M. de Graaf)
- KWR Water Research Institute, Nieuwegein, the Netherlands (G. Elsinga, L. Heijnen, G. Medema)
- University of Edinburgh, Edinburgh, Scotland, UK (L. Lu, S. Lycett)
- Technical University of Denmark, Kongens Lyngby, Denmark (F.M. Aarestrup)
| | - Matthijs Kon
- Erasmus University Medical Center, Rotterdam, the Netherlands (R. Izquierdo-Lara, B.B. Oude Munnink, C.M.E. Schapendonk, D. Nieuwenhuijse, M. Kon, M.P.G. Koopmans, M. de Graaf)
- KWR Water Research Institute, Nieuwegein, the Netherlands (G. Elsinga, L. Heijnen, G. Medema)
- University of Edinburgh, Edinburgh, Scotland, UK (L. Lu, S. Lycett)
- Technical University of Denmark, Kongens Lyngby, Denmark (F.M. Aarestrup)
| | - Lu Lu
- Erasmus University Medical Center, Rotterdam, the Netherlands (R. Izquierdo-Lara, B.B. Oude Munnink, C.M.E. Schapendonk, D. Nieuwenhuijse, M. Kon, M.P.G. Koopmans, M. de Graaf)
- KWR Water Research Institute, Nieuwegein, the Netherlands (G. Elsinga, L. Heijnen, G. Medema)
- University of Edinburgh, Edinburgh, Scotland, UK (L. Lu, S. Lycett)
- Technical University of Denmark, Kongens Lyngby, Denmark (F.M. Aarestrup)
| | - Frank M. Aarestrup
- Erasmus University Medical Center, Rotterdam, the Netherlands (R. Izquierdo-Lara, B.B. Oude Munnink, C.M.E. Schapendonk, D. Nieuwenhuijse, M. Kon, M.P.G. Koopmans, M. de Graaf)
- KWR Water Research Institute, Nieuwegein, the Netherlands (G. Elsinga, L. Heijnen, G. Medema)
- University of Edinburgh, Edinburgh, Scotland, UK (L. Lu, S. Lycett)
- Technical University of Denmark, Kongens Lyngby, Denmark (F.M. Aarestrup)
| | - Samantha Lycett
- Erasmus University Medical Center, Rotterdam, the Netherlands (R. Izquierdo-Lara, B.B. Oude Munnink, C.M.E. Schapendonk, D. Nieuwenhuijse, M. Kon, M.P.G. Koopmans, M. de Graaf)
- KWR Water Research Institute, Nieuwegein, the Netherlands (G. Elsinga, L. Heijnen, G. Medema)
- University of Edinburgh, Edinburgh, Scotland, UK (L. Lu, S. Lycett)
- Technical University of Denmark, Kongens Lyngby, Denmark (F.M. Aarestrup)
| | | | | | | |
Collapse
|
17
|
Villabruna N, Izquierdo Lara RW, Szarvas J, Koopmans MPG, de Graaf M. Phylogenetic Investigation of Norovirus Transmission between Humans and Animals. Viruses 2020; 12:v12111287. [PMID: 33182775 PMCID: PMC7698157 DOI: 10.3390/v12111287] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 10/19/2020] [Revised: 11/06/2020] [Accepted: 11/06/2020] [Indexed: 01/03/2023] Open
Abstract
Norovirus infections are a leading cause of acute gastroenteritis worldwide, affecting people of all ages. There are 10 norovirus genogroups (GI-GX) that infect humans and animals in a host-specific manner. New variants and genotypes frequently emerge, and their origin is not well understood. One hypothesis is that new human infections may be seeded from an animal reservoir, as human noroviruses have occasionally been detected in animal species. The majority of these sequences were identified as older GII.4 variants, but a variety of other GIIs and GIs have been detected as well. While these sequences share at least 94% nt similarity with human strains, most of them are >98% identical to human strains. The fact that these strains were detected in animals after they had been detected through human surveillance to be already circulating in humans suggests human-to-animal transmission.
Collapse
Affiliation(s)
- Nele Villabruna
- Department of Viroscience, Erasmus MC, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (N.V.); (R.W.I.L.); (M.P.G.K.)
| | - Ray W. Izquierdo Lara
- Department of Viroscience, Erasmus MC, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (N.V.); (R.W.I.L.); (M.P.G.K.)
| | - Judit Szarvas
- Research Group for Genomic Epidemiology, Division for Global Surveillance, National Food Institute, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
| | - Marion P. G. Koopmans
- Department of Viroscience, Erasmus MC, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (N.V.); (R.W.I.L.); (M.P.G.K.)
| | - Miranda de Graaf
- Department of Viroscience, Erasmus MC, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (N.V.); (R.W.I.L.); (M.P.G.K.)
- Correspondence:
| |
Collapse
|
18
|
Chhabra P, Graaf MD, Parra GI, Chan MCW, Green K, Martella V, Wang Q, White PA, Katayama K, Vennema H, Koopmans MPG, Vinjé J. Corrigendum: Updated classification of norovirus genogroups and genotypes. J Gen Virol 2020; 101:893. [PMID: 32854814 DOI: 10.1099/jgv.0.001475] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Preeti Chhabra
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Miranda de Graaf
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Gabriel I Parra
- Division of Viral Products, Food and Drug Administration, Silver Spring, MD, USA
| | - Martin Chi-Wai Chan
- Department of Microbiology, Stanley Ho Centre for Emerging Infectious Diseases and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, PR China
| | - Kim Green
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari Aldo Moro, Bari, Italy
| | - Qiuhong Wang
- Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH, USA
| | - Peter A White
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney 2052, Australia
| | - Kazuhiko Katayama
- Laboratory of Viral infection I, Kitasato Institute for Life Sciences Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Harry Vennema
- Division for Virology, Centre for Infectious Diseases Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| |
Collapse
|
19
|
Lamers MM, Beumer J, van der Vaart J, Knoops K, Puschhof J, Breugem TI, Ravelli RBG, Paul van Schayck J, Mykytyn AZ, Duimel HQ, van Donselaar E, Riesebosch S, Kuijpers HJH, Schipper D, van de Wetering WJ, de Graaf M, Koopmans M, Cuppen E, Peters PJ, Haagmans BL, Clevers H. SARS-CoV-2 productively infects human gut enterocytes. Science 2020; 369:50-54. [PMID: 32358202 DOI: 10.1101/2020.04.25.060350] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 04/29/2020] [Indexed: 05/28/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause coronavirus disease 2019 (COVID-19), an influenza-like disease that is primarily thought to infect the lungs with transmission through the respiratory route. However, clinical evidence suggests that the intestine may present another viral target organ. Indeed, the SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) is highly expressed on differentiated enterocytes. In human small intestinal organoids (hSIOs), enterocytes were readily infected by SARS-CoV and SARS-CoV-2, as demonstrated by confocal and electron microscopy. Enterocytes produced infectious viral particles, whereas messenger RNA expression analysis of hSIOs revealed induction of a generic viral response program. Therefore, the intestinal epithelium supports SARS-CoV-2 replication, and hSIOs serve as an experimental model for coronavirus infection and biology.
Collapse
Affiliation(s)
- Mart M Lamers
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Joep Beumer
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Netherlands
| | - Jelte van der Vaart
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Netherlands
| | - Kèvin Knoops
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Jens Puschhof
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Netherlands
| | - Tim I Breugem
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Raimond B G Ravelli
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - J Paul van Schayck
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Anna Z Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Hans Q Duimel
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Elly van Donselaar
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Samra Riesebosch
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Helma J H Kuijpers
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Debby Schipper
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Willine J van de Wetering
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Miranda de Graaf
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Marion Koopmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Centre Utrecht, Utrecht, Netherlands
- Hartwig Medical Foundation, Amsterdam, Netherlands
| | - Peter J Peters
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Bart L Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Netherlands.
| |
Collapse
|
20
|
Lamers MM, Beumer J, van der Vaart J, Knoops K, Puschhof J, Breugem TI, Ravelli RBG, Paul van Schayck J, Mykytyn AZ, Duimel HQ, van Donselaar E, Riesebosch S, Kuijpers HJH, Schipper D, van de Wetering WJ, de Graaf M, Koopmans M, Cuppen E, Peters PJ, Haagmans BL, Clevers H. SARS-CoV-2 productively infects human gut enterocytes. Science 2020; 369:50-54. [PMID: 32358202 PMCID: PMC7199907 DOI: 10.1126/science.abc1669] [Citation(s) in RCA: 1189] [Impact Index Per Article: 297.3] [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: 04/09/2020] [Accepted: 04/29/2020] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause coronavirus disease 2019 (COVID-19), an influenza-like disease that is primarily thought to infect the lungs with transmission through the respiratory route. However, clinical evidence suggests that the intestine may present another viral target organ. Indeed, the SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) is highly expressed on differentiated enterocytes. In human small intestinal organoids (hSIOs), enterocytes were readily infected by SARS-CoV and SARS-CoV-2, as demonstrated by confocal and electron microscopy. Enterocytes produced infectious viral particles, whereas messenger RNA expression analysis of hSIOs revealed induction of a generic viral response program. Therefore, the intestinal epithelium supports SARS-CoV-2 replication, and hSIOs serve as an experimental model for coronavirus infection and biology.
Collapse
Affiliation(s)
- Mart M Lamers
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Joep Beumer
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Netherlands
| | - Jelte van der Vaart
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Netherlands
| | - Kèvin Knoops
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Jens Puschhof
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Netherlands
| | - Tim I Breugem
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Raimond B G Ravelli
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - J Paul van Schayck
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Anna Z Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Hans Q Duimel
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Elly van Donselaar
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Samra Riesebosch
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Helma J H Kuijpers
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Debby Schipper
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Willine J van de Wetering
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Miranda de Graaf
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Marion Koopmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Centre Utrecht, Utrecht, Netherlands
- Hartwig Medical Foundation, Amsterdam, Netherlands
| | - Peter J Peters
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Bart L Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Netherlands.
| |
Collapse
|
21
|
Desdouits M, de Graaf M, Strubbia S, Oude Munnink BB, Kroneman A, Le Guyader FS, Koopmans MPG. Novel opportunities for NGS-based one health surveillance of foodborne viruses. One Health Outlook 2020; 2:14. [PMID: 33829135 PMCID: PMC7993515 DOI: 10.1186/s42522-020-00015-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/01/2020] [Indexed: 05/15/2023]
Abstract
Foodborne viral infections rank among the top 5 causes of disease, with noroviruses and hepatitis A causing the greatest burden globally. Contamination of foods by infected food handlers or through environmental pollution are the main sources of foodborne illness, with a lesser role for consumption of products from infected animals. Viral partial genomic sequencing has been used for more than two decades to track foodborne outbreaks and whole genome or metagenomics next-generation-sequencing (NGS) are new additions to the toolbox of food microbiology laboratories. We discuss developments in the field of targeted and metagenomic NGS, with an emphasis on application in food virology, the challenges and possible solutions towards future routine application.
Collapse
Affiliation(s)
- Marion Desdouits
- IFREMER, Laboratoire de Microbiologie, LSEM/SG2M, Nantes, France
| | - Miranda de Graaf
- Viroscience Department, Erasmus Medical Centre, Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Sofia Strubbia
- IFREMER, Laboratoire de Microbiologie, LSEM/SG2M, Nantes, France
| | - Bas B. Oude Munnink
- Viroscience Department, Erasmus Medical Centre, Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Annelies Kroneman
- Centre for Infectious Disease Control, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | | | - Marion P. G. Koopmans
- Viroscience Department, Erasmus Medical Centre, Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| |
Collapse
|
22
|
Chhabra P, de Graaf M, Parra GI, Chan MCW, Green K, Martella V, Wang Q, White PA, Katayama K, Vennema H, Koopmans MPG, Vinjé J. Updated classification of norovirus genogroups and genotypes. J Gen Virol 2020; 100:1393-1406. [PMID: 31483239 DOI: 10.1099/jgv.0.001318] [Citation(s) in RCA: 440] [Impact Index Per Article: 110.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Noroviruses are genetically diverse RNA viruses associated with acute gastroenteritis in mammalian hosts. Phylogenetically, they can be segregated into different genogroups as well as P (polymerase)-groups and further into genotypes and P-types based on amino acid diversity of the complete VP1 gene and nucleotide diversity of the RNA-dependent RNA polymerase (RdRp) region of ORF1, respectively. In recent years, several new noroviruses have been reported that warrant an update of the existing classification scheme. Using previously described 2× standard deviation (sd) criteria to group sequences into separate clusters, we expanded the number of genogroups to 10 (GI-GX) and the number of genotypes to 48 (9 GI, 27 GII, 3 GIII, 2 GIV, 2 GV, 2 GVI and 1 genotype each for GVII, GVIII, GIX [formerly GII.15] and GX). Viruses for which currently only one sequence is available in public databases were classified into tentative new genogroups (GNA1 and GNA2) and genotypes (GII.NA1, GII.NA2 and GIV.NA1) with their definitive assignment awaiting additional related sequences. Based on nucleotide diversity in the RdRp region, noroviruses can be divided into 60 P-types (14 GI, 37 GII, 2 GIII, 1 GIV, 2 GV, 2 GVI, 1 GVII and 1 GX), 2 tentative P-groups and 14 tentative P-types. Future classification and nomenclature updates will be based on complete genome sequences and will be coordinated and disseminated by the international norovirus classification-working group.
Collapse
Affiliation(s)
- Preeti Chhabra
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Miranda de Graaf
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Gabriel I Parra
- Division of Viral Products, Food and Drug Administration, Silver Spring, MD, USA
| | - Martin Chi-Wai Chan
- Department of Microbiology, Stanley Ho Centre for Emerging Infectious Diseases and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, PR China
| | - Kim Green
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari Aldo Moro, Bari, Italy
| | - Qiuhong Wang
- Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH, USA
| | - Peter A White
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney 2052, Australia
| | - Kazuhiko Katayama
- Laboratory of Viral infection I, Kitasato Institute for Life Sciences Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Harry Vennema
- Division for Virology, Centre for Infectious Diseases Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| |
Collapse
|
23
|
Teesing GR, Erasmus V, Petrignani M, Koopmans MPG, de Graaf M, Vos MC, Klaassen CHW, Verduijn-Leenman A, Schols JMGA, Richardus JH, Voeten HACM. Improving Hand Hygiene Compliance in Nursing Homes: Protocol for a Cluster Randomized Controlled Trial (HANDSOME Study). JMIR Res Protoc 2020; 9:e17419. [PMID: 32356772 PMCID: PMC7229527 DOI: 10.2196/17419] [Citation(s) in RCA: 10] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/20/2020] [Accepted: 02/26/2020] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Hand hygiene compliance is considered the most (cost-)effective measure for preventing health care-associated infections. While hand hygiene interventions have frequently been implemented and assessed in hospitals, there is limited knowledge about hand hygiene compliance in other health care settings and which interventions and implementation methods are effective. OBJECTIVE This study aims to evaluate the effect of a multimodal intervention to increase hand hygiene compliance of nurses in nursing homes through a cluster randomized controlled trial (HANDSOME study). METHODS Nursing homes were randomly allocated to 1 of 3 trial arms: receiving the intervention at a predetermined date, receiving the identical intervention after an infectious disease outbreak, or serving as a control arm. Hand hygiene was evaluated in nursing homes by direct observation at 4 timepoints. We documented compliance with the World Health Organization's 5 moments of hand hygiene, specifically before touching a patient, before a clean/aseptic procedure, after body fluid exposure risk, after touching a patient, and after touching patient surroundings. The primary outcome is hand hygiene compliance of the nurses to the standards of the World Health Organization. The secondary outcome is infectious disease incidence among residents. Infectious disease incidence was documented by a staff member at each nursing home unit. Outcomes will be compared with the presence of norovirus, rhinovirus, and Escherichia coli on surfaces in the nursing homes, as measured using quantitative polymerase chain reaction. RESULTS The study was funded in September 2015. Data collection started in October 2016 and was completed in October 2017. Data analysis will be completed in 2020. CONCLUSIONS HANDSOME studies the effectiveness of a hand hygiene intervention specifically for the nursing home environment. Nurses were taught the World Health Organization's 5 moments of hand hygiene guidelines using the slogan "Room In, Room Out, Before Clean, After Dirty," which was developed for nursing staff to better understand and remember the hygiene guidelines. HANDSOME should contribute to improved hand hygiene practice and a reduction in infectious disease rates and related mortality. TRIAL REGISTRATION Netherlands Trial Register (NTR6188) NL6049; https://www.trialregister.nl/trial/6049. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/17419.
Collapse
Affiliation(s)
- Gwen R Teesing
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Municipal Public Health Service Rotterdam-Rijnmond, Rotterdam, Netherlands
| | - Vicki Erasmus
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Mariska Petrignani
- Municipal Public Health Service Haaglanden, Den Haag, Netherlands.,Municipal Public Health Service Amsterdam, Amsterdam, Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Margreet C Vos
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Corné H W Klaassen
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | | | - Jos M G A Schols
- Department of Health Services Research and Department of Family Medicine, Maastricht University, Maastricht, Netherlands
| | - Jan Hendrik Richardus
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Municipal Public Health Service Rotterdam-Rijnmond, Rotterdam, Netherlands
| | - Helene A C M Voeten
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Municipal Public Health Service Rotterdam-Rijnmond, Rotterdam, Netherlands
| |
Collapse
|
24
|
Sips GJ, Dirven MJG, Donkervoort JT, van Kolfschoten FM, Schapendonk CME, Phan MVT, Bloem A, van Leeuwen AF, Trompenaars ME, Koopmans MPG, van der Eijk AA, de Graaf M, Fanoy EB. Norovirus outbreak in a natural playground: A One Health approach. Zoonoses Public Health 2020; 67:453-459. [PMID: 32037743 PMCID: PMC7318310 DOI: 10.1111/zph.12689] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 06/18/2019] [Revised: 12/24/2019] [Accepted: 01/10/2020] [Indexed: 12/03/2022]
Abstract
Norovirus constitutes the most frequently identified infectious cause of disease outbreaks associated with untreated recreational water. When investigating outbreaks related to surface water, a One Health approach is insightful. Historically, there has been a focus on potential contamination of recreational water by bird droppings and a recent publication demonstrating human noroviruses in bird faeces suggested this should be investigated in future water‐related norovirus outbreaks. Here, we describe a One Health approach investigating a norovirus outbreak in a natural playground. On social media, a large amount of waterfowl were reported to defecate near these playground premises leading to speculations about their potential involvement. Surface water, as well as human and bird faecal specimens, was tested for human noroviruses. Norovirus was found to be the most likely cause of the outbreak but there was no evidence for transmission via waterfowl. Cases had become known on social media prior to notification to the public health service underscoring the potential of online media as an early warning system. In view of known risk factors, advice was given for future outbreak investigations and natural playground design.
Collapse
Affiliation(s)
- Gregorius J Sips
- Public Health Service Rotterdam-Rijnmond, Rotterdam, The Netherlands.,Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | | | | | | | - My V T Phan
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Annemieke Bloem
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | | | - Marion P G Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Miranda de Graaf
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ewout B Fanoy
- Public Health Service Rotterdam-Rijnmond, Rotterdam, The Netherlands
| |
Collapse
|
25
|
Strubbia S, Schaeffer J, Oude Munnink BB, Besnard A, Phan MVT, Nieuwenhuijse DF, de Graaf M, Schapendonk CME, Wacrenier C, Cotten M, Koopmans MPG, Le Guyader FS. Metavirome Sequencing to Evaluate Norovirus Diversity in Sewage and Related Bioaccumulated Oysters. Front Microbiol 2019; 10:2394. [PMID: 31681246 PMCID: PMC6811496 DOI: 10.3389/fmicb.2019.02394] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/03/2019] [Indexed: 12/20/2022] Open
Abstract
Metagenomic sequencing is a promising method to determine the virus diversity in environmental samples such as sewage or shellfish. However, to identify the short RNA genomes of human enteric viruses among the large diversity of nucleic acids present in such complex matrices, method optimization is still needed. This work presents methodological developments focused on norovirus, a small ssRNA non-enveloped virus known as the major cause of human gastroenteritis worldwide and frequently present in human excreta and sewage. Different elution protocols were applied and Illumina MiSeq technology were used to study norovirus diversity. A double approach, agnostic deep sequencing and a capture-based approach (VirCapSeq-VERT) was used to identify norovirus in environmental samples. Family-specific viral contigs were classified and sorted by SLIM and final norovirus contigs were genotyped using the online Norovirus genotyping tool v2.0. From sewage samples, 14 norovirus genogroup I sequences were identified of which six were complete genomes. For norovirus genogroup II, nine sequences were identified and three of them comprised more than half of the genome. In oyster samples bioaccumulated with these sewage samples, only the use of an enrichment step during library preparation allowed successful identification of nine different sequences of norovirus genogroup I and four for genogroup II (>500 bp). This study demonstrates the importance of method development to increase virus recovery, and the interest of a capture-based approach to be able to identify viruses present at low concentrations.
Collapse
Affiliation(s)
- Sofia Strubbia
- Laboratoire de Microbiologie, LSEM-SG2M-RBE, Ifremer, Nantes, France
| | - Julien Schaeffer
- Laboratoire de Microbiologie, LSEM-SG2M-RBE, Ifremer, Nantes, France
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Alban Besnard
- Laboratoire de Microbiologie, LSEM-SG2M-RBE, Ifremer, Nantes, France
| | - My V T Phan
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - David F Nieuwenhuijse
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Candice Wacrenier
- Laboratoire de Microbiologie, LSEM-SG2M-RBE, Ifremer, Nantes, France
| | - Matthew Cotten
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | | |
Collapse
|
26
|
van Beek J, de Graaf M, Smits S, Schapendonk CME, Verjans GMGM, Vennema H, van der Eijk AA, Phan MVT, Cotten M, Koopmans M. Whole-Genome Next-Generation Sequencing to Study Within-Host Evolution of Norovirus (NoV) Among Immunocompromised Patients With Chronic NoV Infection. J Infect Dis 2019; 216:1513-1524. [PMID: 29029115 DOI: 10.1093/infdis/jix520] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 09/22/2017] [Indexed: 01/29/2023] Open
Abstract
Background The genus Norovirus comprises large genetic diversity, and new GII.4 variants emerge every 2-3 years. It is unknown in which host these new variants originate. Here we study whether prolonged shedders within the immunocompromised population could be a reservoir for newly emerging strains. Methods Sixty-five fecal samples from 16 immunocompromised patients were retrospectively selected. Isolated viral RNA was enriched by hybridization with a custom norovirus whole-genome RNA bait set and deep sequenced on the Illumina MiSeq platform. Results Patients shed virus for average 352 days (range, 76-716 days). Phylogenetic analysis showed distinct GII.4 variants in 3 of 13 patients (23%). The viral mutation rates were variable between patients but did not differ between various immune status groups. All within-host GII.4 viral populations showed amino acid changes at blocking epitopes over time, and the majority of VP1 amino acid mutations were located at the capsid surface. Conclusions This study found viruses in immunocompromised hosts that are genetically distinct from viruses circulating in the general population, and these patients therefore may contain a reservoir for newly emerging strains. Future studies need to determine whether these new strains are of risk to other immunocompromised patients and the general population.
Collapse
Affiliation(s)
- Janko van Beek
- Department of Viroscience, Erasmus Medical Center, Bilthoven, the Netherlands.,Center for Infectious Diseases Research, Diagnostics, and Screening, National Institute of Public Health and the Environment, Bilthoven, the Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus Medical Center, Bilthoven, the Netherlands
| | - Saskia Smits
- Department of Viroscience, Erasmus Medical Center, Bilthoven, the Netherlands.,Viroclinics Biosciences, Rotterdam, Bilthoven, the Netherlands
| | | | | | - Harry Vennema
- Center for Infectious Diseases Research, Diagnostics, and Screening, National Institute of Public Health and the Environment, Bilthoven, the Netherlands
| | | | - My V T Phan
- Department of Viroscience, Erasmus Medical Center, Bilthoven, the Netherlands
| | - Matthew Cotten
- Department of Viroscience, Erasmus Medical Center, Bilthoven, the Netherlands
| | - Marion Koopmans
- Department of Viroscience, Erasmus Medical Center, Bilthoven, the Netherlands
| |
Collapse
|
27
|
Petrignani M, Verhoef L, de Graaf M, Richardus JH, Koopmans M. Chronic sequelae and severe complications of norovirus infection: A systematic review of literature. J Clin Virol 2018; 105:1-10. [PMID: 29804008 DOI: 10.1016/j.jcv.2018.05.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 04/23/2018] [Accepted: 05/11/2018] [Indexed: 11/17/2022]
Abstract
Norovirus causes an estimated 18% of all cases of acute gastroenteritis worldwide and is found to be associated with mortality. To create a first overview of severe complications and chronic sequelae of norovirus infections, a systematic review of literature was performed. Of 3928 individual hits, 176 publications remained for data extraction. Study periods varied between 1974 and 2017, though strongly skewed towards the last decade (n = 122, 70%). Countries of studies were worldwide, though Africa, and Carribean, Central and South America were underrepresented. Strong evidence was found for chronic diarrhea in immunocompromised patients, affecting 9%-100% of investigated cohorts. The duration of chronic diarrhea varied from four weeks up to nine years, leading to either wasting, weight loss or failure to thrive in a third of the reported cases (224). Other complications with significant evidence were necrotizing enterocolitis (NEC) in preterm infants associated with norovirus infection (8 papers), and benign infantile convulsions with gastroenteritis (BICG; 19 papers). Studies on norovirus infection and inflammatory bowel disease (IBD) mostly concluded against this association (5 of 7). The remaining papers mentioned a large variety of possible sequelae or complications. Based on the available literature, chronic norovirus diarrhea is the major sequela of norovirus infection in primary immune deficient, oncologic and transplant patients. Norovirus infection - like other gastrointestinal pathogens - can cause a range of sequelae and complications, and should be considered in the differential diagnosis of these manifestations.
Collapse
Affiliation(s)
- Mariska Petrignani
- Municipal Public Health Service Rotterdam-Rijnmond, Rotterdam, The Netherlands.
| | - Linda Verhoef
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jan Hendrik Richardus
- Public Health Department, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| |
Collapse
|
28
|
Chan MCW, Hu Y, Chen H, Podkolzin AT, Zaytseva EV, Komano J, Sakon N, Poovorawan Y, Vongpunsawad S, Thanusuwannasak T, Hewitt J, Croucher D, Collins N, Vinjé J, Pang XL, Lee BE, de Graaf M, van Beek J, Vennema H, Koopmans MPG, Niendorf S, Poljsak-Prijatelj M, Steyer A, White PA, Lun JH, Mans J, Hung TN, Kwok K, Cheung K, Lee N, Chan PKS. Global Spread of Norovirus GII.17 Kawasaki 308, 2014-2016. Emerg Infect Dis 2018; 23:1359-1354. [PMID: 28726618 PMCID: PMC5547775 DOI: 10.3201/eid2308.161138] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Analysis of complete capsid sequences of the emerging norovirus GII.17 Kawasaki 308 from 13 countries demonstrated that they originated from a single haplotype since the initial emergence in China in late 2014. Global spread of a sublineage SL2 was identified. A new sublineage SL3 emerged in China in 2016.
Collapse
|
29
|
de Graaf M, Bodewes R, van Elk CE, van de Bildt M, Getu S, Aron GI, Verjans GMGM, Osterhaus ADME, van den Brand JMA, Kuiken T, Koopmans MPG. Norovirus Infection in Harbor Porpoises. Emerg Infect Dis 2018; 23:87-91. [PMID: 27983498 PMCID: PMC5176230 DOI: 10.3201/eid2301.161081] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
A norovirus was detected in harbor porpoises, a previously unknown host for norovirus. This norovirus had low similarity to any known norovirus. Viral RNA was detected primarily in intestinal tissue, and specific serum antibodies were detected in 8 (24%) of 34 harbor porpoises from the North Sea.
Collapse
|
30
|
van Beek J, de Graaf M, Al-Hello H, Allen DJ, Ambert-Balay K, Botteldoorn N, Brytting M, Buesa J, Cabrerizo M, Chan M, Cloak F, Di Bartolo I, Guix S, Hewitt J, Iritani N, Jin M, Johne R, Lederer I, Mans J, Martella V, Maunula L, McAllister G, Niendorf S, Niesters HG, Podkolzin AT, Poljsak-Prijatelj M, Rasmussen LD, Reuter G, Tuite G, Kroneman A, Vennema H, Koopmans MPG. Molecular surveillance of norovirus, 2005-16: an epidemiological analysis of data collected from the NoroNet network. Lancet Infect Dis 2018; 18:545-553. [PMID: 29396001 DOI: 10.1016/s1473-3099(18)30059-8] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 11/02/2017] [Accepted: 11/16/2017] [Indexed: 11/29/2022]
Abstract
BACKGROUND The development of a vaccine for norovirus requires a detailed understanding of global genetic diversity of noroviruses. We analysed their epidemiology and diversity using surveillance data from the NoroNet network. METHODS We included genetic sequences of norovirus specimens obtained from outbreak investigations and sporadic gastroenteritis cases between 2005 and 2016 in Europe, Asia, Oceania, and Africa. We genotyped norovirus sequences and analysed sequences that overlapped at open reading frame (ORF) 1 and ORF2. Additionally, we assessed the sampling date and country of origin of the first reported sequence to assess when and where novel drift variants originated. FINDINGS We analysed 16 635 norovirus sequences submitted between Jan 1, 2005, to Nov 17, 2016, of which 1372 (8·2%) sequences belonged to genotype GI, 15 256 (91·7%) to GII, and seven (<0·1%) to GIV.1. During this period, 26 different norovirus capsid genotypes circulated and 22 different recombinant genomes were found. GII.4 drift variants emerged with 2-3-year periodicity up to 2012, but not afterwards. Instead, the GII.4 Sydney capsid seems to persist through recombination, with a novel recombinant of GII.P16-GII.4 Sydney 2012 variant detected in 2014 in Germany (n=1) and the Netherlands (n=1), and again in 2016 in Japan (n=2), China (n=8), and the Netherlands (n=3). The novel GII.P17-GII.17, first reported in Asia in 2014, has circulated widely in Europe in 2015-16 (GII.P17 made up a highly variable proportion of all sequences in each country [median 11·3%, range 4·2-53·9], as did GII.17 [median 6·3%, range 0-44·5]). GII.4 viruses were more common in outbreaks in health-care settings (2239 [37·2%] of 6022 entries) compared with other genotypes (101 [12·5%] of 809 entries for GI and 263 [13·5%] of 1941 entries for GII non-GII.Pe-GII.4 or GII.P4-GII.4). INTERPRETATION Continuous changes in the global norovirus genetic diversity highlight the need for sustained global norovirus surveillance, including assessment of possible immune escape and evolution by recombination, to provide a full overview of norovirus epidemiology for future vaccine policy decisions. FUNDING European Union's Horizon 2020 grant COMPARE, ZonMw TOP grant, the Virgo Consortium funded by the Dutch Government, and the Hungarian Scientific Research Fund.
Collapse
Affiliation(s)
- Janko van Beek
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands; Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute of Public Health and the Environment, Bilthoven, Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Haider Al-Hello
- Department of Health Security, National Institute for Health and Welfare, Helsinki, Finland
| | - David J Allen
- Virus Reference Department, Public Health England, London, UK; Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Health Protection Research Unit in Gastrointestinal Infections, National Institute for Health Research, UK
| | - Katia Ambert-Balay
- National Reference Centre for Gastroenteritis Viruses, University Hospital of Dijon Bourgogne, Dijon, France; AgroSup Dijon PAM UMR A 02.102, University Bourgogne Franche-Comté, Dijon, France
| | - Nadine Botteldoorn
- Scientific Service of Foodborne Pathogens, Institute of Public Health, Brussels, Belgium
| | - Mia Brytting
- Microbial Typing Unit, The Public Health Agency of Sweden, Stockholm, Sweden
| | - Javier Buesa
- Viral Gastroenteritis Research Group, Department of Microbiology, University of Valencia, Valencia, Spain
| | - Maria Cabrerizo
- Enterovirus and Viral Gastroenteritis Unit, Instituto de Salud Carlos III, Madrid, Spain; Translational Research Network in Pediatric Infectious Diseases, Instituto de Investigación Sanitaria de la Paz, Madrid, Spain
| | - Martin Chan
- Department of Microbiology, Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region, China
| | - Fiona Cloak
- Gastroenteric, Vectorborne and Zoonotic Unit, Health Protection Surveillance Centre, Dublin, Ireland
| | - Ilaria Di Bartolo
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanita, Rome, Italy
| | - Susana Guix
- Enteric Virus Laboratory, University of Barcelona, Barcelona, Spain
| | - Joanne Hewitt
- Norovirus Reference Laboratory, Institute of Environmental Science and Research, Porirua, New Zealand
| | - Nobuhiro Iritani
- Department of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Miao Jin
- Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China, Beijing, China
| | - Reimar Johne
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Ingeborg Lederer
- Reference Centres and Reference Laboratories, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Janet Mans
- Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari, Bari, Italy
| | - Leena Maunula
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | | | - Sandra Niendorf
- Consultant Laboratory for Noroviruses, Robert Koch Institute, Berlin, Germany
| | - Hubert G Niesters
- Department of Medical Microbiology, Division of Clinical Virology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Alexander T Podkolzin
- RussianFederal Service for Surveillance on Consumer Rights Protection and Human Wellbeing (Rospotrebnadzor), Central Research Institute of Epidemiology, Moscow, Russia
| | - Mateja Poljsak-Prijatelj
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Lasse Dam Rasmussen
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Gábor Reuter
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Gráinne Tuite
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Annelies Kroneman
- Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute of Public Health and the Environment, Bilthoven, Netherlands
| | - Harry Vennema
- Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute of Public Health and the Environment, Bilthoven, Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands; Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute of Public Health and the Environment, Bilthoven, Netherlands.
| | | |
Collapse
|
31
|
de Graaf M, Villabruna N, Koopmans MP. Capturing norovirus transmission. Curr Opin Virol 2017; 22:64-70. [PMID: 28056379 DOI: 10.1016/j.coviro.2016.11.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/18/2016] [Accepted: 11/21/2016] [Indexed: 12/15/2022]
Abstract
Human norovirus is a leading cause of gastroenteritis and is efficiently transmitted between humans and around the globe. The burden of norovirus infections in the global community and in health-care settings warrant the availability of outbreak prevention strategies and control measures that are tailored to the pathogen, outbreak setting and population at risk. A better understanding of viral and host determinants of transmission would aid in developing and fine-tuning such efforts. Here, we describe mechanisms of transmission, available model systems for studying norovirus transmission and their strengths and weaknesses as well as future research strategies.
Collapse
Affiliation(s)
- Miranda de Graaf
- Department of Viroscience, Erasmus Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
| | - Nele Villabruna
- Department of Viroscience, Erasmus Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Marion Pg Koopmans
- Department of Viroscience, Erasmus Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| |
Collapse
|
32
|
de Graaf M, Beck R, Caccio SM, Duim B, Fraaij PLA, Le Guyader FS, Lecuit M, Le Pendu J, de Wit E, Schultsz C. Sustained fecal-oral human-to-human transmission following a zoonotic event. Curr Opin Virol 2016; 22:1-6. [PMID: 27888698 PMCID: PMC7102779 DOI: 10.1016/j.coviro.2016.11.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 11/01/2016] [Accepted: 11/03/2016] [Indexed: 12/28/2022]
Abstract
Bacterial, viral and parasitic zoonotic pathogens that transmit via the fecal-oral route have a major impact on global health. However, the mechanisms underlying the emergence of such pathogens from the animal reservoir and their persistence in the human population are poorly understood. Here, we present a framework of human-to-human transmission of zoonotic pathogens that considers the factors relevant for fecal-oral human-to-human transmission route at the levels of host, pathogen, and environment. We discuss current data gaps and propose future research directions.
Collapse
Affiliation(s)
- Miranda de Graaf
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Relja Beck
- Department for Bacteriology and Parasitology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Simone M Caccio
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Birgitta Duim
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands; WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
| | - Pieter LA Fraaij
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Pediatrics, Erasmus Medical Center-Sophia, Rotterdam, The Netherlands
| | | | - Marc Lecuit
- Institut Pasteur, Inserm U1117, Biology of Infection Unit, Paris, France; Paris Descartes University, Sorbonne Paris Cité, Necker-Pasteur Centre for Infectiology, Necker-Enfants Malades University Hospital, Institut Imagine, Assistance Publique-Hôpitaux de Paris, Paris, France
| | | | - Emmie de Wit
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Constance Schultsz
- Department of Global Health and Department of Medical Microbiology, Academic Medical Center, Amsterdam, The Netherlands.
| |
Collapse
|
33
|
van Beek J, de Graaf M, Xia M, Jiang X, Vinjé J, Beersma M, de Bruin E, van de Vijver D, Holwerda M, van Houten M, Buisman AM, van Binnendijk R, Osterhaus ADME, van der Klis F, Vennema H, Koopmans MPG. Comparison of norovirus genogroup I, II and IV seroprevalence among children in the Netherlands, 1963, 1983 and 2006. J Gen Virol 2016; 97:2255-2264. [PMID: 27365054 PMCID: PMC5042128 DOI: 10.1099/jgv.0.000533] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [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] [Indexed: 11/18/2022] Open
Abstract
Noroviruses are a major cause of acute gastroenteritis worldwide and are a genetically diverse group of viruses. Since 2002, an increasing number of norovirus outbreaks have been reported globally, but it is not clear whether this increase has been caused by a higher awareness or reflects the emergence of new genogroup II genotype 4 (GII.4) variants. The hypothesis that norovirus prevalence has increased post-2002 and is related to the emergence of GII.4 is tested in this study. Sera collected from children aged <5 years of three Dutch cross-sectional population based cohorts in 1963, 1983 and 2006/2007 (n=143, n=130 and n=376, respectively) were tested for specific serum IgG by protein array using antigens to GII.4 and a range of other antigens representing norovirus GI, GII and GIV genotypes. The protein array was validated by paired sera of norovirus infected patients and supernatants of B-cell cultures with single epitope specificity. Evidence for norovirus infection was found to be common among Dutch children in each cohort, but the prevalence towards different genotypes changed over time. At the genogroup level, GI seroprevalence decreased significantly between 1963 and 2006/2007, while a significant increase of GII and, in particular, specific antibodies of the genotype GII.4 was detected in the 2006/2007 cohort. There were no children with only GII.4 antibodies in the 1963 cohort. This study shows that the high GII.4 norovirus incidence in very young children is a recent phenomenon. These findings are of importance for vaccine development and trials that are currently focusing mostly on GII.4 viruses.
Collapse
Affiliation(s)
- Janko van Beek
- Department of Viroscience, Erasmus Medical Center, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands.,Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute of Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Miranda de Graaf
- Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute of Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Ming Xia
- Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Ave, Cincinnati, OH 45229, USA
| | - Xi Jiang
- Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Ave, Cincinnati, OH 45229, USA
| | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA 30333, USA
| | - Mathias Beersma
- Department of Viroscience, Erasmus Medical Center, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - Erwin de Bruin
- Department of Viroscience, Erasmus Medical Center, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands.,Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute of Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - David van de Vijver
- Department of Viroscience, Erasmus Medical Center, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - Melle Holwerda
- Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute of Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Marlies van Houten
- Pediatric Department, Spaarne Hospital Hoofddorp, Hoofddorp, The Netherlands
| | - Annemarie M Buisman
- Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute of Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Rob van Binnendijk
- Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute of Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Albert D M E Osterhaus
- Department of Viroscience, Erasmus Medical Center, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - Fiona van der Klis
- Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute of Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Harry Vennema
- Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute of Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Marion P G Koopmans
- Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute of Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands.,Department of Viroscience, Erasmus Medical Center, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| |
Collapse
|
34
|
|
35
|
Spronken MI, Short KR, Herfst S, Bestebroer TM, Vaes VP, van der Hoeven B, Koster AJ, Kremers GJ, Scott DP, Gultyaev AP, Sorell EM, de Graaf M, Bárcena M, Rimmelzwaan GF, Fouchier RA. Optimisations and Challenges Involved in the Creation of Various Bioluminescent and Fluorescent Influenza A Virus Strains for In Vitro and In Vivo Applications. PLoS One 2015; 10:e0133888. [PMID: 26241861 PMCID: PMC4524686 DOI: 10.1371/journal.pone.0133888] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [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: 05/07/2015] [Accepted: 07/03/2015] [Indexed: 01/15/2023] Open
Abstract
Bioluminescent and fluorescent influenza A viruses offer new opportunities to study influenza virus replication, tropism and pathogenesis. To date, several influenza A reporter viruses have been described. These strategies typically focused on a single reporter gene (either bioluminescent or fluorescent) in a single virus backbone. However, whilst bioluminescence is suited to in vivo imaging, fluorescent viruses are more appropriate for microscopy. Therefore, the idea l reporter virus varies depending on the experiment in question, and it is important that any reporter virus strategy can be adapted accordingly. Herein, a strategy was developed to create five different reporter viruses in a single virus backbone. Specifically, enhanced green fluorescent protein (eGFP), far-red fluorescent protein (fRFP), near-infrared fluorescent protein (iRFP), Gaussia luciferase (gLUC) and firefly luciferase (fLUC) were inserted into the PA gene segment of A/PR/8/34 (H1N1). This study provides a comprehensive characterisation of the effects of different reporter genes on influenza virus replication and reporter activity. In vivo reporter gene expression, in lung tissues, was only detected for eGFP, fRFP and gLUC expressing viruses. In vitro, the eGFP-expressing virus displayed the best reporter stability and could be used for correlative light electron microscopy (CLEM). This strategy was then used to create eGFP-expressing viruses consisting entirely of pandemic H1N1, highly pathogenic avian influenza (HPAI) H5N1 and H7N9. The HPAI H5N1 eGFP-expressing virus infected mice and reporter gene expression was detected, in lung tissues, in vivo. Thus, this study provides new tools and insights for the creation of bioluminescent and fluorescent influenza A reporter viruses.
Collapse
Affiliation(s)
- Monique I. Spronken
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Kirsty R. Short
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
- School of Biomedical Sciences, University of Queensland, Brisbane, Australia
| | - Sander Herfst
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Theo M. Bestebroer
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Vincent P. Vaes
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Barbara van der Hoeven
- Department of Molecular Cell Biology, Section Electron Microscopy, Leiden University Medical Centre, Leiden, the Netherlands
| | - Abraham J. Koster
- Department of Molecular Cell Biology, Section Electron Microscopy, Leiden University Medical Centre, Leiden, the Netherlands
| | - Gert-Jan Kremers
- Erasmus Optical Imaging Centre, Department of Pathology, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Dana P. Scott
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States of America
| | - Alexander P. Gultyaev
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
- Leiden Institute of Advanced Computer Science, Leiden University, Leiden, the Netherlands
| | - Erin M. Sorell
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
- Milken Institute School of Public Health, Department of Health Policy and Management, George Washington University, Washington, DC, United States of America
| | - Miranda de Graaf
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Montserrat Bárcena
- Department of Molecular Cell Biology, Section Electron Microscopy, Leiden University Medical Centre, Leiden, the Netherlands
| | - Guus F. Rimmelzwaan
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Ron A. Fouchier
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
- * E-mail:
| |
Collapse
|
36
|
Lewis NS, Verhagen JH, Javakhishvili Z, Russell CA, Lexmond P, Westgeest KB, Bestebroer TM, Halpin RA, Lin X, Ransier A, Fedorova NB, Stockwell TB, Latorre-Margalef N, Olsen B, Smith G, Bahl J, Wentworth DE, Waldenström J, Fouchier RAM, de Graaf M. Influenza A virus evolution and spatio-temporal dynamics in Eurasian wild birds: a phylogenetic and phylogeographical study of whole-genome sequence data. J Gen Virol 2015; 96:2050-2060. [PMID: 25904147 PMCID: PMC4681060 DOI: 10.1099/vir.0.000155] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [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] [Indexed: 01/25/2023] Open
Abstract
Low pathogenic avian influenza A viruses (IAVs) have a natural host reservoir in wild waterbirds and the potential to spread to other host species. Here, we investigated the evolutionary, spatial and temporal dynamics of avian IAVs in Eurasian wild birds. We used whole-genome sequences collected as part of an intensive long-term Eurasian wild bird surveillance study, and combined this genetic data with temporal and spatial information to explore the virus evolutionary dynamics. Frequent reassortment and co-circulating lineages were observed for all eight genomic RNA segments over time. There was no apparent species-specific effect on the diversity of the avian IAVs. There was a spatial and temporal relationship between the Eurasian sequences and significant viral migration of avian IAVs from West Eurasia towards Central Eurasia. The observed viral migration patterns differed between segments. Furthermore, we discuss the challenges faced when analysing these surveillance and sequence data, and the caveats to be borne in mind when drawing conclusions from the apparent results of such analyses.
Collapse
Affiliation(s)
- Nicola S Lewis
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Josanne H Verhagen
- Department of Viroscience, Erasmus MC, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Zurab Javakhishvili
- Institute of Ecology, Ilia State University, 3/5 Cholokashvili, Tbilisi, Georgia
| | - Colin A Russell
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Pascal Lexmond
- Department of Viroscience, Erasmus MC, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Kim B Westgeest
- Department of Viroscience, Erasmus MC, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Theo M Bestebroer
- Department of Viroscience, Erasmus MC, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | | | - Xudong Lin
- J. Craig Venter Institute, Rockville, MD, 20850, USA
| | - Amy Ransier
- J. Craig Venter Institute, Rockville, MD, 20850, USA
| | | | | | - Neus Latorre-Margalef
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden.,Department of Population Health, College of Veterinary Medicine, Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, GA, 30602, USA
| | - Björn Olsen
- Department of Medical Sciences, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Gavin Smith
- Laboratory of Virus Evolution, Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore
| | - Justin Bahl
- Laboratory of Virus Evolution, Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore.,Center for Infectious Diseases, The University of Texas School of Public Health, Houston, TX, 77030, USA
| | | | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus MC, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus MC, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| |
Collapse
|
37
|
Westgeest KB, Bestebroer TM, Spronken MIJ, Gao J, Couzens L, Osterhaus ADME, Eichelberger M, Fouchier RAM, de Graaf M. Optimization of an enzyme-linked lectin assay suitable for rapid antigenic characterization of the neuraminidase of human influenza A(H3N2) viruses. J Virol Methods 2015; 217:55-63. [PMID: 25712563 DOI: 10.1016/j.jviromet.2015.02.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 02/06/2015] [Accepted: 02/16/2015] [Indexed: 10/24/2022]
Abstract
Antibodies to neuraminidase (NA), the second most abundant surface protein of the influenza virus, contribute to protection against influenza virus infection. Although traditional and miniaturized thiobarbituric acid (TBA) neuraminidase inhibition (NI) assays have been successfully used to characterize the antigenic properties of NA, these methods are cumbersome and not easily amendable to rapid screening. An additional difficulty of the NI assay is the interference by hemagglutinin (HA)-specific antibodies. To prevent interference of HA-specific antibodies, most NI assays are performed with recombinant viruses containing a mismatched HA. However, generation of these viruses is time consuming and unsuitable for large-scale surveillance. The feasibility of using the recently developed enzyme-linked lectin assay (ELLA) to evaluate the antigenic relatedness of NA of wild type A(H3N2) viruses was assessed. Rather than using recombinant viruses, wild type A(H3N2) viruses were used as antigen with ferret sera elicited against recombinant viruses with a mismatched HA. In this study, details of the critical steps that are needed to modify and optimize the NI ELLA in a format that is reproducible, highly sensitive, and useful for influenza virus surveillance to monitor antigenic drift of NA are provided.
Collapse
Affiliation(s)
- Kim B Westgeest
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Theo M Bestebroer
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Jin Gao
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Laura Couzens
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | | | - Maryna Eichelberger
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
| |
Collapse
|
38
|
Bodewes R, Hapsari R, Rubio García A, Sánchez Contreras GJ, van de Bildt MWG, de Graaf M, Kuiken T, Osterhaus ADME. Molecular epidemiology of seal parvovirus, 1988-2014. PLoS One 2014; 9:e112129. [PMID: 25390639 PMCID: PMC4229121 DOI: 10.1371/journal.pone.0112129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 10/13/2014] [Indexed: 01/30/2023] Open
Abstract
A novel parvovirus was discovered recently in the brain of a harbor seal (Phoca vitulina) with chronic meningo-encephalitis. Phylogenetic analysis of this virus indicated that it belongs to the genus Erythroparvovirus, to which also human parvovirus B19 belongs. In the present study, the prevalence, genetic diversity and clinical relevance of seal parvovirus (SePV) infections was evaluated in both harbor and grey seals (Halichoerus grypus) that lived in Northwestern European coastal waters from 1988 to 2014. To this end, serum and tissue samples collected from seals were tested for the presence of seal parvovirus DNA by real-time PCR and the sequences of the partial NS gene and the complete VP2 gene of positive samples were determined. Seal parvovirus DNA was detected in nine (8%) of the spleen tissues tested and in one (0.5%) of the serum samples tested, including samples collected from seals that died in 1988. Sequence analysis of the partial NS and complete VP2 genes of nine SePV revealed multiple sites with nucleotide substitutions but only one amino acid change in the VP2 gene. Estimated nucleotide substitution rates per year were 2.00 × 10(-4) for the partial NS gene and 1.15 × 10(-4) for the complete VP2 gene. Most samples containing SePV DNA were co-infected with phocine herpesvirus 1 or PDV, so no conclusions could be drawn about the clinical impact of SePV infection alone. The present study is one of the few in which the mutation rates of parvoviruses were evaluated over a period of more than 20 years, especially in a wildlife population, providing additional insights into the genetic diversity of parvoviruses.
Collapse
Affiliation(s)
- Rogier Bodewes
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | | | - Ana Rubio García
- Seal Rehabilitation and Research Centre, Pieterburen, the Netherlands
| | | | | | - Miranda de Graaf
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Thijs Kuiken
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Albert D. M. E. Osterhaus
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
- Viroclinics Biosciences BV, Rotterdam, the Netherlands
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine, Hannover, Germany
- Artemis One Health, Utrecht, the Netherlands
| |
Collapse
|
39
|
Linster M, van Boheemen S, de Graaf M, Schrauwen EJA, Lexmond P, Mänz B, Bestebroer TM, Baumann J, van Riel D, Rimmelzwaan GF, Osterhaus ADME, Matrosovich M, Fouchier RAM, Herfst S. Identification, characterization, and natural selection of mutations driving airborne transmission of A/H5N1 virus. Cell 2014; 157:329-339. [PMID: 24725402 DOI: 10.1016/j.cell.2014.02.040] [Citation(s) in RCA: 203] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 02/17/2014] [Accepted: 02/24/2014] [Indexed: 12/26/2022]
Abstract
Recently, A/H5N1 influenza viruses were shown to acquire airborne transmissibility between ferrets upon targeted mutagenesis and virus passage. The critical genetic changes in airborne A/Indonesia/5/05 were not yet identified. Here, five substitutions proved to be sufficient to determine this airborne transmission phenotype. Substitutions in PB1 and PB2 collectively caused enhanced transcription and virus replication. One substitution increased HA thermostability and lowered the pH of membrane fusion. Two substitutions independently changed HA binding preference from α2,3-linked to α2,6-linked sialic acid receptors. The loss of a glycosylation site in HA enhanced overall binding to receptors. The acquired substitutions emerged early during ferret passage as minor variants and became dominant rapidly. Identification of substitutions that are essential for airborne transmission of avian influenza viruses between ferrets and their associated phenotypes advances our fundamental understanding of virus transmission and will increase the value of future surveillance programs and public health risk assessments.
Collapse
Affiliation(s)
- Martin Linster
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, 3015GE Rotterdam, the Netherlands
| | - Sander van Boheemen
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, 3015GE Rotterdam, the Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, 3015GE Rotterdam, the Netherlands
| | - Eefje J A Schrauwen
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, 3015GE Rotterdam, the Netherlands
| | - Pascal Lexmond
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, 3015GE Rotterdam, the Netherlands
| | - Benjamin Mänz
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, 3015GE Rotterdam, the Netherlands
| | - Theo M Bestebroer
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, 3015GE Rotterdam, the Netherlands
| | - Jan Baumann
- Institute of Virology, Philipps-University, 35043 Marburg, Germany
| | - Debby van Riel
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, 3015GE Rotterdam, the Netherlands
| | - Guus F Rimmelzwaan
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, 3015GE Rotterdam, the Netherlands
| | - Albert D M E Osterhaus
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, 3015GE Rotterdam, the Netherlands
| | | | - Ron A M Fouchier
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, 3015GE Rotterdam, the Netherlands.
| | - Sander Herfst
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, 3015GE Rotterdam, the Netherlands
| |
Collapse
|
40
|
Abstract
Zoonotic influenza A viruses originating from the animal reservoir pose a threat for humans, as they have the ability to trigger pandemics upon adaptation to and invasion of an immunologically naive population. Of particular concern are the H5N1 viruses that continue to circulate in poultry in numerous countries in Europe, Asia and Africa, and the recently emerged H7N9 viruses in China, due to their relatively high number of human fatalities and pandemic potential. To start a pandemic, zoonotic influenza A viruses should not only acquire the ability to attach to, enter and replicate in the critical target cells in the respiratory tract of the new host, but also efficiently spread between humans by aerosol or respiratory droplet transmission. Here, we discuss the latest advances on the genetic and phenotypic determinants required for avian influenza A viruses to adapt to and transmit between mammals.
Collapse
Affiliation(s)
- Mathilde Richard
- Department of Viroscience, Postgraduate School Molecular Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Postgraduate School Molecular Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Sander Herfst
- Department of Viroscience, Postgraduate School Molecular Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| |
Collapse
|
41
|
Abstract
The recent emergence of a novel avian A/H7N9 influenza virus in poultry and humans in China, as well as laboratory studies on adaptation and transmission of avian A/H5N1 influenza viruses, has shed new light on influenza virus adaptation to mammals. One of the biological traits required for animal influenza viruses to cross the species barrier that received considerable attention in animal model studies, in vitro assays, and structural analyses is receptor binding specificity. Sialylated glycans present on the apical surface of host cells can function as receptors for the influenza virus hemagglutinin (HA) protein. Avian and human influenza viruses typically have a different sialic acid (SA)-binding preference and only few amino acid changes in the HA protein can cause a switch from avian to human receptor specificity. Recent experiments using glycan arrays, virus histochemistry, animal models, and structural analyses of HA have added a wealth of knowledge on receptor binding specificity. Here, we review recent data on the interaction between influenza virus HA and SA receptors of the host, and the impact on virus host range, pathogenesis, and transmission. Remaining challenges and future research priorities are also discussed.
Collapse
Affiliation(s)
- Miranda de Graaf
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | | |
Collapse
|
42
|
Martín-Valls GE, Simon-Grifé M, van Boheemen S, de Graaf M, Bestebroer TM, Busquets N, Martín M, Casal J, Fouchier RAM, Mateu E. Phylogeny of Spanish swine influenza viruses isolated from respiratory disease outbreaks and evolution of swine influenza virus within an endemically infected farm. Vet Microbiol 2014; 170:266-77. [PMID: 24685238 DOI: 10.1016/j.vetmic.2014.02.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 02/10/2014] [Accepted: 02/17/2014] [Indexed: 11/28/2022]
Abstract
In the present study, outbreaks of respiratory disease were investigated for the presence of swine influenza virus (SIV). In 14 cases the circulating SIV strains were isolated, fully sequenced and compared with other known SIVs. The viruses causing the outbreaks belonged to the H1N1 (including human pandemic H1N1), H3N2 and H1N2 subtypes. In 11/14 cases the phylogenetic analyses indicated the occurrence of probable reassortment events. In the second part of the study, the genetic evolution of H1N1 SIV was assessed in a longitudinal study in closed groups of pigs over six months. Sequencing of the 22 isolates indicated co-circulation of two different variants for the same virus, as well as the emergence of SIV reassortants at certain time-points. These results indicate that reassortment events in SIV are common, and point towards the need for a better understanding of the epidemiology of SIV, particularly in endemic farms.
Collapse
Affiliation(s)
- Gerard E Martín-Valls
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Meritxell Simon-Grifé
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Sander van Boheemen
- Department of Virology, Erasmus Medical Center, Erasmus University, 3015GE Rotterdam, The Netherlands.
| | - Miranda de Graaf
- Department of Virology, Erasmus Medical Center, Erasmus University, 3015GE Rotterdam, The Netherlands.
| | - Theo M Bestebroer
- Department of Virology, Erasmus Medical Center, Erasmus University, 3015GE Rotterdam, The Netherlands.
| | - Núria Busquets
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Margarita Martín
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain; Departament de Sanitat i Anatomia animals, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Spain.
| | - Jordi Casal
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain; Departament de Sanitat i Anatomia animals, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Spain.
| | - Ron A M Fouchier
- Department of Virology, Erasmus Medical Center, Erasmus University, 3015GE Rotterdam, The Netherlands.
| | - Enric Mateu
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain; Departament de Sanitat i Anatomia animals, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Spain.
| |
Collapse
|
43
|
van Riel D, Leijten LME, de Graaf M, Siegers JY, Short KR, Spronken MIJ, Schrauwen EJA, Fouchier RAM, Osterhaus ADME, Kuiken T. Novel avian-origin influenza A (H7N9) virus attaches to epithelium in both upper and lower respiratory tract of humans. Am J Pathol 2013; 183:1137-1143. [PMID: 24029490 PMCID: PMC3791677 DOI: 10.1016/j.ajpath.2013.06.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 06/21/2013] [Accepted: 06/28/2013] [Indexed: 12/20/2022]
Abstract
Influenza A viruses from animal reservoirs have the capacity to adapt to humans and cause influenza pandemics. The occurrence of an influenza pandemic requires efficient virus transmission among humans, which is associated with virus attachment to the upper respiratory tract. Pandemic severity depends on virus ability to cause pneumonia, which is associated with virus attachment to the lower respiratory tract. Recently, a novel avian-origin H7N9 influenza A virus with unknown pandemic potential emerged in humans. We determined the pattern of attachment of two genetically engineered viruses containing the hemagglutinin of either influenza virus A/Shanghai/1/13 or A/Anhui/1/13 to formalin-fixed human respiratory tract tissues using histochemical analysis. Our results show that the emerging H7N9 virus attached moderately or abundantly to both upper and lower respiratory tract, a pattern not seen before for avian influenza A viruses. With the caveat that virus attachment is only the first step in the virus replication cycle, these results suggest that the emerging H7N9 virus has the potential both to transmit efficiently among humans and to cause severe pneumonia.
Collapse
Affiliation(s)
- Debby van Riel
- Department of Viroscience, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Lonneke M E Leijten
- Department of Viroscience, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Jurre Y Siegers
- Department of Viroscience, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Kirsty R Short
- Department of Viroscience, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Monique I J Spronken
- Department of Viroscience, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Eefje J A Schrauwen
- Department of Viroscience, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Albert D M E Osterhaus
- Department of Viroscience, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Thijs Kuiken
- Department of Viroscience, Erasmus University Medical Centre, Rotterdam, The Netherlands.
| |
Collapse
|
44
|
Trilling M, Bellora N, Rutkowski AJ, de Graaf M, Dickinson P, Robertson K, Prazeres da Costa O, Ghazal P, Friedel CC, Albà MM, Dölken L. Deciphering the modulation of gene expression by type I and II interferons combining 4sU-tagging, translational arrest and in silico promoter analysis. Nucleic Acids Res 2013; 41:8107-25. [PMID: 23832230 PMCID: PMC3783172 DOI: 10.1093/nar/gkt589] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [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: 04/01/2013] [Revised: 05/30/2013] [Accepted: 06/12/2013] [Indexed: 01/14/2023] Open
Abstract
Interferons (IFN) play a pivotal role in innate immunity, orchestrating a cell-intrinsic anti-pathogenic state and stimulating adaptive immune responses. The complex interplay between the primary response to IFNs and its modulation by positive and negative feedback loops is incompletely understood. Here, we implement the combination of high-resolution gene-expression profiling of nascent RNA with translational inhibition of secondary feedback by cycloheximide. Unexpectedly, this approach revealed a prominent role of negative feedback mechanisms during the immediate (≤60 min) IFNα response. In contrast, a more complex picture involving both negative and positive feedback loops was observed on IFNγ treatment. IFNγ-induced repression of genes associated with regulation of gene expression, cellular development, apoptosis and cell growth resulted from cycloheximide-resistant primary IFNγ signalling. In silico promoter analysis revealed significant overrepresentation of SP1/SP3-binding sites and/or GC-rich stretches. Although signal transducer and activator of transcription 1 (STAT1)-binding sites were not overrepresented, repression was lost in absence of STAT1. Interestingly, basal expression of the majority of these IFNγ-repressed genes was dependent on STAT1 in IFN-naïve fibroblasts. Finally, IFNγ-mediated repression was also found to be evident in primary murine macrophages. IFN-repressed genes include negative regulators of innate and stress response, and their decrease may thus aid the establishment of a signalling perceptive milieu.
Collapse
Affiliation(s)
- Mirko Trilling
- Institute for Virology, University Hospital in Essen, University of Duisburg-Essen, Essen, D-45147, Germany, Computational Genomics Group, IMIM-UPF Research Programme on Biomedical Informatics, Barcelona Biomedical Research Park (PRBB), Barcelona 08003, Spain, Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK, Division of Pathway Medicine, University of Edinburgh Medical School, Edinburgh, EH16 4SB, Scotland, UK, SynthSys, University of Edinburgh, Edinburgh, EH9 3JU Scotland, UK, Institute of Medical Microbiology, Technical University Munich, Munich 81675, Germany, Institute for Informatics, Ludwig-Maximilians-University Munich, Munich 80333, Germany and Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
| | - Nicolás Bellora
- Institute for Virology, University Hospital in Essen, University of Duisburg-Essen, Essen, D-45147, Germany, Computational Genomics Group, IMIM-UPF Research Programme on Biomedical Informatics, Barcelona Biomedical Research Park (PRBB), Barcelona 08003, Spain, Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK, Division of Pathway Medicine, University of Edinburgh Medical School, Edinburgh, EH16 4SB, Scotland, UK, SynthSys, University of Edinburgh, Edinburgh, EH9 3JU Scotland, UK, Institute of Medical Microbiology, Technical University Munich, Munich 81675, Germany, Institute for Informatics, Ludwig-Maximilians-University Munich, Munich 80333, Germany and Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
| | - Andrzej J. Rutkowski
- Institute for Virology, University Hospital in Essen, University of Duisburg-Essen, Essen, D-45147, Germany, Computational Genomics Group, IMIM-UPF Research Programme on Biomedical Informatics, Barcelona Biomedical Research Park (PRBB), Barcelona 08003, Spain, Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK, Division of Pathway Medicine, University of Edinburgh Medical School, Edinburgh, EH16 4SB, Scotland, UK, SynthSys, University of Edinburgh, Edinburgh, EH9 3JU Scotland, UK, Institute of Medical Microbiology, Technical University Munich, Munich 81675, Germany, Institute for Informatics, Ludwig-Maximilians-University Munich, Munich 80333, Germany and Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
| | - Miranda de Graaf
- Institute for Virology, University Hospital in Essen, University of Duisburg-Essen, Essen, D-45147, Germany, Computational Genomics Group, IMIM-UPF Research Programme on Biomedical Informatics, Barcelona Biomedical Research Park (PRBB), Barcelona 08003, Spain, Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK, Division of Pathway Medicine, University of Edinburgh Medical School, Edinburgh, EH16 4SB, Scotland, UK, SynthSys, University of Edinburgh, Edinburgh, EH9 3JU Scotland, UK, Institute of Medical Microbiology, Technical University Munich, Munich 81675, Germany, Institute for Informatics, Ludwig-Maximilians-University Munich, Munich 80333, Germany and Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
| | - Paul Dickinson
- Institute for Virology, University Hospital in Essen, University of Duisburg-Essen, Essen, D-45147, Germany, Computational Genomics Group, IMIM-UPF Research Programme on Biomedical Informatics, Barcelona Biomedical Research Park (PRBB), Barcelona 08003, Spain, Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK, Division of Pathway Medicine, University of Edinburgh Medical School, Edinburgh, EH16 4SB, Scotland, UK, SynthSys, University of Edinburgh, Edinburgh, EH9 3JU Scotland, UK, Institute of Medical Microbiology, Technical University Munich, Munich 81675, Germany, Institute for Informatics, Ludwig-Maximilians-University Munich, Munich 80333, Germany and Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
| | - Kevin Robertson
- Institute for Virology, University Hospital in Essen, University of Duisburg-Essen, Essen, D-45147, Germany, Computational Genomics Group, IMIM-UPF Research Programme on Biomedical Informatics, Barcelona Biomedical Research Park (PRBB), Barcelona 08003, Spain, Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK, Division of Pathway Medicine, University of Edinburgh Medical School, Edinburgh, EH16 4SB, Scotland, UK, SynthSys, University of Edinburgh, Edinburgh, EH9 3JU Scotland, UK, Institute of Medical Microbiology, Technical University Munich, Munich 81675, Germany, Institute for Informatics, Ludwig-Maximilians-University Munich, Munich 80333, Germany and Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
| | - Olivia Prazeres da Costa
- Institute for Virology, University Hospital in Essen, University of Duisburg-Essen, Essen, D-45147, Germany, Computational Genomics Group, IMIM-UPF Research Programme on Biomedical Informatics, Barcelona Biomedical Research Park (PRBB), Barcelona 08003, Spain, Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK, Division of Pathway Medicine, University of Edinburgh Medical School, Edinburgh, EH16 4SB, Scotland, UK, SynthSys, University of Edinburgh, Edinburgh, EH9 3JU Scotland, UK, Institute of Medical Microbiology, Technical University Munich, Munich 81675, Germany, Institute for Informatics, Ludwig-Maximilians-University Munich, Munich 80333, Germany and Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
| | - Peter Ghazal
- Institute for Virology, University Hospital in Essen, University of Duisburg-Essen, Essen, D-45147, Germany, Computational Genomics Group, IMIM-UPF Research Programme on Biomedical Informatics, Barcelona Biomedical Research Park (PRBB), Barcelona 08003, Spain, Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK, Division of Pathway Medicine, University of Edinburgh Medical School, Edinburgh, EH16 4SB, Scotland, UK, SynthSys, University of Edinburgh, Edinburgh, EH9 3JU Scotland, UK, Institute of Medical Microbiology, Technical University Munich, Munich 81675, Germany, Institute for Informatics, Ludwig-Maximilians-University Munich, Munich 80333, Germany and Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
| | - Caroline C. Friedel
- Institute for Virology, University Hospital in Essen, University of Duisburg-Essen, Essen, D-45147, Germany, Computational Genomics Group, IMIM-UPF Research Programme on Biomedical Informatics, Barcelona Biomedical Research Park (PRBB), Barcelona 08003, Spain, Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK, Division of Pathway Medicine, University of Edinburgh Medical School, Edinburgh, EH16 4SB, Scotland, UK, SynthSys, University of Edinburgh, Edinburgh, EH9 3JU Scotland, UK, Institute of Medical Microbiology, Technical University Munich, Munich 81675, Germany, Institute for Informatics, Ludwig-Maximilians-University Munich, Munich 80333, Germany and Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
| | - M. Mar Albà
- Institute for Virology, University Hospital in Essen, University of Duisburg-Essen, Essen, D-45147, Germany, Computational Genomics Group, IMIM-UPF Research Programme on Biomedical Informatics, Barcelona Biomedical Research Park (PRBB), Barcelona 08003, Spain, Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK, Division of Pathway Medicine, University of Edinburgh Medical School, Edinburgh, EH16 4SB, Scotland, UK, SynthSys, University of Edinburgh, Edinburgh, EH9 3JU Scotland, UK, Institute of Medical Microbiology, Technical University Munich, Munich 81675, Germany, Institute for Informatics, Ludwig-Maximilians-University Munich, Munich 80333, Germany and Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
| | - Lars Dölken
- Institute for Virology, University Hospital in Essen, University of Duisburg-Essen, Essen, D-45147, Germany, Computational Genomics Group, IMIM-UPF Research Programme on Biomedical Informatics, Barcelona Biomedical Research Park (PRBB), Barcelona 08003, Spain, Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK, Division of Pathway Medicine, University of Edinburgh Medical School, Edinburgh, EH16 4SB, Scotland, UK, SynthSys, University of Edinburgh, Edinburgh, EH9 3JU Scotland, UK, Institute of Medical Microbiology, Technical University Munich, Munich 81675, Germany, Institute for Informatics, Ludwig-Maximilians-University Munich, Munich 80333, Germany and Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
| |
Collapse
|
45
|
Richard M, Schrauwen EJA, de Graaf M, Bestebroer TM, Spronken MIJ, van Boheemen S, de Meulder D, Lexmond P, Linster M, Herfst S, Smith DJ, van den Brand JM, Burke DF, Kuiken T, Rimmelzwaan GF, Osterhaus ADME, Fouchier RAM. Limited airborne transmission of H7N9 influenza A virus between ferrets. Nature 2013; 501:560-3. [PMID: 23925116 PMCID: PMC3819191 DOI: 10.1038/nature12476] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 07/17/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Mathilde Richard
- Department of Viroscience, Erasmus Medical Center, 3015GE Rotterdam, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Wilks S, de Graaf M, Smith DJ, Burke DF. A review of influenza haemagglutinin receptor binding as it relates to pandemic properties. Vaccine 2012; 30:4369-76. [PMID: 22682293 DOI: 10.1016/j.vaccine.2012.02.076] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Revised: 01/14/2012] [Accepted: 02/27/2012] [Indexed: 01/29/2023]
Abstract
Haemagglutinin is a determinant of many viral properties, and successful adaptation to a human-like form is thought to be an important step toward pandemic influenza emergence. The availability of structurally distinct sialic acid linked receptors in the sites of human and avian influenza infection are generally held to account for the differences observed, but the relevance of other selection pressures has not been elucidated. There is evidence for genetic and structural constraints of haemagglutinin playing a role in restricting haemagglutinin adaptation, and also for differences in the selection pressure to alter binding, specifically when considering virus replication within host compared to transmission between hosts. Understanding which characteristics underlie such adaptations in humans is now possible in greater detail by using glycan arrays. However, results from these assays must also interpreted in context of an as yet still to be determined detailed knowledge of the structural diversity of sialic acids in the human respiratory tract. A clearer understanding of the evolutionary benefits conveyed by different haemagglutinin properties would have substantial impact and would affect the risk we allocate to viral propagation in different species, such as swine and poultry. Relevant to the H5N1 threat, current evidence also suggests that mortality associated with any emergent pandemic from current strains may be reduced if haemagglutinin specificity changes, further emphasising the importance of understanding how and if selection pressures in the human will cause such an alteration.
Collapse
Affiliation(s)
- Sam Wilks
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, United Kingdom
| | | | | | | |
Collapse
|
47
|
Marcinowski L, Lidschreiber M, Windhager L, Rieder M, Bosse JB, Rädle B, Bonfert T, Györy I, de Graaf M, da Costa OP, Rosenstiel P, Friedel CC, Zimmer R, Ruzsics Z, Dölken L. Real-time transcriptional profiling of cellular and viral gene expression during lytic cytomegalovirus infection. PLoS Pathog 2012; 8:e1002908. [PMID: 22969428 PMCID: PMC3435240 DOI: 10.1371/journal.ppat.1002908] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [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: 02/22/2012] [Accepted: 08/01/2012] [Indexed: 01/08/2023] Open
Abstract
During viral infections cellular gene expression is subject to rapid alterations induced by both viral and antiviral mechanisms. In this study, we applied metabolic labeling of newly transcribed RNA with 4-thiouridine (4sU-tagging) to dissect the real-time kinetics of cellular and viral transcriptional activity during lytic murine cytomegalovirus (MCMV) infection. Microarray profiling on newly transcribed RNA obtained at different times during the first six hours of MCMV infection revealed discrete functional clusters of cellular genes regulated with distinct kinetics at surprising temporal resolution. Immediately upon virus entry, a cluster of NF-κB- and interferon-regulated genes was induced. Rapid viral counter-regulation of this coincided with a very transient DNA-damage response, followed by a delayed ER-stress response. Rapid counter-regulation of all three clusters indicated the involvement of novel viral regulators targeting these pathways. In addition, down-regulation of two clusters involved in cell-differentiation (rapid repression) and cell-cycle (delayed repression) was observed. Promoter analysis revealed all five clusters to be associated with distinct transcription factors, of which NF-κB and c-Myc were validated to precisely match the respective transcriptional changes observed in newly transcribed RNA. 4sU-tagging also allowed us to study the real-time kinetics of viral gene expression in the absence of any interfering virion-associated-RNA. Both qRT-PCR and next-generation sequencing demonstrated a sharp peak of viral gene expression during the first two hours of infection including transcription of immediate-early, early and even well characterized late genes. Interestingly, this was subject to rapid gene silencing by 5–6 hours post infection. Despite the rapid increase in viral DNA load during viral DNA replication, transcriptional activity of some viral genes remained remarkably constant until late-stage infection, or was subject to further continuous decline. In summary, this study pioneers real-time transcriptional analysis during a lytic herpesvirus infection and highlights numerous novel regulatory aspects of virus-host-cell interaction. Cytomegaloviruses are large DNA viruses, which establish life-long latent infections, leaving the infected individual at risk of reactivation and disease. Here, we applied 4-thiouridine-(4sU)-tagging of newly transcribed RNA to monitor the real-time kinetics of transcriptional activity of both cellular and viral genes during lytic murine CMV (MCMV) infection. We observed a cascade of MCMV-induced signaling events including a rapid inflammatory/interferon-response, a transient DNA-damage-response and a delayed ER-stress-response. All of these were heavily counter-regulated by viral gene expression. Besides dramatically increasing temporal resolution, our approach provides the unique opportunity to study viral transcriptional activity in absence of any interfering virion-associated-RNA. Virion-associated-RNA consists of transcripts that are unspecifically incorporated into the virus particles thereby resembling the cellular RNA profile of late stage infection. A clear picture of which viral genes are expressed, particularly at very early times of infection, could thus not be obtained. By overcoming this problem, we provide intriguing insights into the regulation of viral gene expression, namely 1) a peak of viral gene expression during the first two hours of infection including the expression of well-characterized late genes and 2) remarkably constant or even continuously declining expression of some viral genes despite the onset of rapid viral DNA replication.
Collapse
Affiliation(s)
- Lisa Marcinowski
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University, Munich, Germany
| | - Michael Lidschreiber
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University, Munich, Germany
| | - Lukas Windhager
- Institute for Informatics, Ludwig-Maximilians-University, Munich, Germany
| | - Martina Rieder
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University, Munich, Germany
| | - Jens B. Bosse
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Bernd Rädle
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University, Munich, Germany
| | - Thomas Bonfert
- Institute for Informatics, Ludwig-Maximilians-University, Munich, Germany
| | - Ildiko Györy
- School of Biomedical and Biological Sciences, Centre for Research in Translational Biomedicine, Plymouth University, Plymouth, United Kingdom
| | - Miranda de Graaf
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | | | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | | | - Ralf Zimmer
- Institute for Informatics, Ludwig-Maximilians-University, Munich, Germany
| | - Zsolt Ruzsics
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University, Munich, Germany
| | - Lars Dölken
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University, Munich, Germany
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
- * E-mail:
| |
Collapse
|
48
|
Westgeest KB, de Graaf M, Fourment M, Bestebroer TM, van Beek R, Spronken MIJ, de Jong JC, Rimmelzwaan GF, Russell CA, Osterhaus ADME, Smith GJD, Smith DJ, Fouchier RAM. Genetic evolution of the neuraminidase of influenza A (H3N2) viruses from 1968 to 2009 and its correspondence to haemagglutinin evolution. J Gen Virol 2012; 93:1996-2007. [PMID: 22718569 DOI: 10.1099/vir.0.043059-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Each year, influenza viruses cause epidemics by evading pre-existing humoral immunity through mutations in the major glycoproteins: the haemagglutinin (HA) and the neuraminidase (NA). In 2004, the antigenic evolution of HA of human influenza A (H3N2) viruses was mapped (Smith et al., Science 305, 371-376, 2004) from its introduction in humans in 1968 until 2003. The current study focused on the genetic evolution of NA and compared it with HA using the dataset of Smith and colleagues, updated to the epidemic of the 2009/2010 season. Phylogenetic trees and genetic maps were constructed to visualize the genetic evolution of NA and HA. The results revealed multiple reassortment events over the years. Overall rates of evolutionary change were lower for NA than for HA1 at the nucleotide level. Selection pressures were estimated, revealing an abundance of negatively selected sites and sparse positively selected sites. The differences found between the evolution of NA and HA1 warrant further analysis of the evolution of NA at the phenotypic level, as has been done previously for HA.
Collapse
Affiliation(s)
- Kim B Westgeest
- Department of Virology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
| | - Miranda de Graaf
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK.,Department of Virology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
| | - Mathieu Fourment
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore
| | - Theo M Bestebroer
- Department of Virology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
| | - Ruud van Beek
- Department of Virology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
| | - Monique I J Spronken
- Department of Virology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
| | - Jan C de Jong
- Department of Virology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
| | - Guus F Rimmelzwaan
- Department of Virology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
| | - Colin A Russell
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA.,Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | | | - Gavin J D Smith
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore
| | - Derek J Smith
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA.,Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK.,Department of Virology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
| | - Ron A M Fouchier
- Department of Virology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
| |
Collapse
|
49
|
van Velzen M, van Loenen FB, Meesters RJW, de Graaf M, Remeijer L, Luider TM, Osterhaus ADME, Verjans GMGM. Latent acyclovir-resistant herpes simplex virus type 1 in trigeminal ganglia of immunocompetent individuals. J Infect Dis 2012; 205:1539-43. [PMID: 22457282 DOI: 10.1093/infdis/jis237] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Specific mutations within the hypervariable herpes simplex virus (HSV) gene thymidine kinase (TK) gene lead to acyclovir (ACV) resistance. To uncover the existence of latent ACV-resistant (ACV(R)) HSV-1, we determined the genetic and functional variability of the HSV-1 TK gene pool in paired trigeminal ganglia (TG) of 5 immunocompetent individuals. The latent virus pool consisted of a donor-specific HSV-1 quasispecies, including one major ACV-sensitive (ACV(S)) and multiple phylogenetic-related minor ACV(S) and ACV(R) TK variants. Contrary to minor variants, major TK variants were shared between paired TG. The data demonstrate the coexistence of phylogenetic-related ACV(S) and ACV(R) latent HSV-1 in human TG.
Collapse
Affiliation(s)
- Monique van Velzen
- Department of Virology, Laboratory of Neuro-Oncology and Clinical and Cancer Proteomics, Erasmus Medical Center, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Garten RJ, Davis CT, Russell CA, Shu B, Lindstrom S, Balish A, Sessions WM, Xu X, Skepner E, Deyde V, Okomo-Adhiambo M, Gubareva L, Barnes J, Smith CB, Emery SL, Hillman MJ, Rivailler P, Smagala J, de Graaf M, Burke DF, Fouchier RAM, Pappas C, Alpuche-Aranda CM, López-Gatell H, Olivera H, López I, Myers CA, Faix D, Blair PJ, Yu C, Keene KM, Dotson PD, Boxrud D, Sambol AR, Abid SH, St George K, Bannerman T, Moore AL, Stringer DJ, Blevins P, Demmler-Harrison GJ, Ginsberg M, Kriner P, Waterman S, Smole S, Guevara HF, Belongia EA, Clark PA, Beatrice ST, Donis R, Katz J, Finelli L, Bridges CB, Shaw M, Jernigan DB, Uyeki TM, Smith DJ, Klimov AI, Cox NJ. Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans. Science 2009; 325:197-201. [PMID: 19465683 PMCID: PMC3250984 DOI: 10.1126/science.1176225] [Citation(s) in RCA: 1771] [Impact Index Per Article: 118.1] [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] [Indexed: 12/16/2022]
Abstract
Since its identification in April 2009, an A(H1N1) virus containing a unique combination of gene segments from both North American and Eurasian swine lineages has continued to circulate in humans. The lack of similarity between the 2009 A(H1N1) virus and its nearest relatives indicates that its gene segments have been circulating undetected for an extended period. Its low genetic diversity suggests that the introduction into humans was a single event or multiple events of similar viruses. Molecular markers predictive of adaptation to humans are not currently present in 2009 A(H1N1) viruses, suggesting that previously unrecognized molecular determinants could be responsible for the transmission among humans. Antigenically the viruses are homogeneous and similar to North American swine A(H1N1) viruses but distinct from seasonal human A(H1N1).
Collapse
MESH Headings
- Animals
- Antibodies, Viral/immunology
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Disease Outbreaks
- Evolution, Molecular
- Genes, Viral
- Genetic Variation
- Genome, Viral
- Hemagglutination Inhibition Tests
- Hemagglutinin Glycoproteins, Influenza Virus/chemistry
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Humans
- Influenza A Virus, H1N1 Subtype/classification
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A virus/genetics
- Influenza, Human/epidemiology
- Influenza, Human/immunology
- Influenza, Human/virology
- Mutation
- Neuraminidase/genetics
- Orthomyxoviridae Infections/veterinary
- Orthomyxoviridae Infections/virology
- Phylogeny
- Reassortant Viruses/genetics
- Swine
- Swine Diseases/virology
- Viral Matrix Proteins/genetics
- Viral Nonstructural Proteins/genetics
Collapse
Affiliation(s)
- Rebecca J Garten
- WHO Collaborating Center for Influenza, Centers for Disease Control and Prevention (CDC), Atlanta, GA 30333, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|