17 results on '"Vennema, Harry"'
Search Results
2. Increased risk of infection with SARS-CoV-2 Omicron BA.1 compared with Delta in vaccinated and previously infected individuals, the Netherlands, 22 November 2021 to 19 January 2022
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Eggink, Dirk, Andeweg, Stijn P, Vennema, Harry, van Maarseveen, Noortje, Vermaas, Klaas, Vlaemynck, Boris, Schepers, Raf, van Gageldonk-Lafeber, Arianne B, van den Hof, Susan, Reusken, Chantal Bem, and Knol, Mirjam J
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air-borne infections ,vaccines and immunisation ,viral infections ,severe acute respiratory syndrome - SARS ,SARS-CoV-2 Omicron Variant of Concern Vaccine escape ,epidemiology ,laboratory - Published
- 2022
3. Norovirus Illness Is a Global Problem: Emergence and Spread of Norovirus GII4. Variants, 2001-2007
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Siebenga, J. Joukje, Vennema, Harry, Zheng, Du-Ping, Vinjé, Jan, Lee, Bonita E., Pang, Xiao-Li, Ho, Eric C. M., Lim, Wilina, Choudekar, Avinash, Broor, Shobha, Halperin, Tamar, Rasool, Nassar B. G., Hewitt, Joanne, Greening, Gail E., Jin, Miao, Duan, Zhao-Jun, Lucero, Yalda, O'Ryan, Miguel, Hoehne, Marina, Schreier, Eckart, Ratcliff, Rodney M., White, Peter A., Iritani, Nobuhiro, Reuter, Gábor, and Koopmans, Marion
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- 2009
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4. Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands
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Oude Munnink, Bas B., Nieuwenhuijse, David F., Stein, Mart, O’Toole, Áine, Haverkate, Manon, Mollers, Madelief, Kamga, Sandra K., Schapendonk, Claudia, Pronk, Mark, Lexmond, Pascal, van der Linden, Anne, Bestebroer, Theo, Chestakova, Irina, Overmars, Ronald J., van Nieuwkoop, Stefan, Molenkamp, Richard, van der Eijk, Annemiek A., GeurtsvanKessel, Corine, Vennema, Harry, Meijer, Adam, Rambaut, Andrew, van Dissel, Jaap, Sikkema, Reina S., Timen, Aura, Koopmans, Marion, Oudehuis, G. J. A. P. M., Schinkel, Janke, Kluytmans, Jan, Kluytmans-van den Bergh, Marjolein, van den Bijllaardt, Wouter, Berntvelsen, Robbert G., van Rijen, Miranda M. L., Schneeberger, Peter, Pas, Suzan, Diederen, Bram M., Bergmans, Anneke M. C., van der Eijk, P. A. Verspui, Verweij, Jaco J., Buiting, Anton G. N., Streefkerk, Roel, Aldenkamp, A. P., de Man, P., Koelemal, J. G. M., Ong, D., Paltansing, S., Veassen, N., Sleven, Jacqueline, Bakker, Leendert, Brockhoff, Heinrich, Rietveld, Ariene, Slijkerman Megelink, Fred, Cohen Stuart, James, de Vries, Anne, van der Reijden, Wil, Ros, A., Lodder, Esther, Verspui-van der Eijk, Ellen, Huijskens, Inge, Kraan, E. M., van der Linden, M. P. M., Debast, S. B., Naiemi, N. Al, Kroes, A. C. M., Damen, Marjolein, Dinant, Sander, Lekkerkerk, Sybren, Pontesilli, Oscar, Smit, Pieter, van Tienen, Carla, Godschalk, P. C. R., van Pelt, Jorien, Ott, Alewijn, van der Weijden, Charlie, Wertheim, Heiman, Rahamat-Langendoen, Janette, Reimerink, Johan, Bodewes, Rogier, Duizer, Erwin, van der Veer, Bas, Reusken, Chantal, Lutgens, Suzanne, Hermans, Mirjam, Wever, P., Leenders, A., ter Waarbeek, Henriette, Hoebe, Christian, Medical Microbiology and Infection Prevention, AII - Infectious diseases, Virology, RS: CAPHRI - R4 - Health Inequities and Societal Participation, and Med Microbiol, Infect Dis & Infect Prev
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0301 basic medicine ,medicine.medical_specialty ,Molecular biology ,Clinical Decision-Making ,Pneumonia, Viral ,Genome, Viral ,medicine.disease_cause ,Disease cluster ,General Biochemistry, Genetics and Molecular Biology ,Betacoronavirus ,03 medical and health sciences ,0302 clinical medicine ,SDG 3 - Good Health and Well-being ,Environmental health ,Pandemic ,Epidemiology ,medicine ,Humans ,Author Correction ,Pandemics ,Netherlands ,Coronavirus ,Respiratory tract diseases ,Whole Genome Sequencing ,biology ,SARS-CoV-2 ,Transmission (medicine) ,Public health ,COVID-19 ,Outbreak ,Genomics ,General Medicine ,biology.organism_classification ,3. Good health ,030104 developmental biology ,Geography ,ZIKA ,030220 oncology & carcinogenesis ,VIRUS ,Public Health ,Coronavirus Infections - Abstract
In late December 2019, a cluster of cases of pneumonia of unknown etiology were reported linked to a market in Wuhan, China1. The causative agent was identified as the speciesSevere acute respiratory syndrome-related coronavirusand was named SARS-CoV-2 (ref. 2). By 16 April the virus had spread to 185 different countries, infected over 2,000,000 people and resulted in over 130,000 deaths3. In the Netherlands, the first case of SARS-CoV-2 was notified on 27 February. The outbreak started with several different introductory events from Italy, Austria, Germany and France followed by local amplification in, and later also outside, the south of the Netherlands. The combination of near to real-time whole-genome sequence analysis and epidemiology resulted in reliable assessments of the extent of SARS-CoV-2 transmission in the community, facilitating early decision-making to control local transmission of SARS-CoV-2 in the Netherlands. We demonstrate how these data were generated and analyzed, and how SARS-CoV-2 whole-genome sequencing, in combination with epidemiological data, was used to inform public health decision-making in the Netherlands. Metastava project.
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- 2020
5. Rapid SARS-CoV-2 whole genome sequencing for informed public health decision making in the Netherlands
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Oude Munnink, Bas B., Nieuwenhuijse, David F., Stein, Mart, O’Toole, Áine, Haverkate, Manon, Mollers, Madelief, Kamga, Sandra K., Schapendonk, Claudia, Pronk, Mark, Lexmond, Pascal, van der Linden, Anne, Bestebroer, Theo, Chestakova, Irina, Overmars, Ronald J., van Nieuwkoop, Stefan, Molenkamp, Richard, van der Eijk, Annemiek, GeurtsvanKessel, Corine, Vennema, Harry, Meijer, Adam, Rambaut, Andrew, van Dissel, Jaap, Sikkema, Reina S., Timen, Aura, and Koopmans, Marion
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Whole genome sequencing ,0303 health sciences ,medicine.medical_specialty ,030306 microbiology ,Public health ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,viruses ,fungi ,Outbreak ,virus diseases ,medicine.disease_cause ,Genome ,3. Good health ,law.invention ,body regions ,03 medical and health sciences ,Transmission (mechanics) ,Geography ,law ,Environmental health ,Epidemiology ,medicine ,skin and connective tissue diseases ,030304 developmental biology ,Coronavirus - Abstract
SARS-CoV-2 is a novel coronavirus that has rapidly spread across the globe. In the Netherlands, the first case of SARS-CoV-2 has been notified on the 27th of February. Here, we describe the first three weeks of the SARS-CoV-2 outbreak in the Netherlands, which started with several different introductory events from Italy, Austria, Germany and France followed by local amplification in, and later also, outside the South of the Netherlands. The timely generation of whole genome sequences combined with epidemiological investigations facilitated early decision making in an attempt to control local transmission of SARS-CoV-2 in the Netherlands.
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- 2020
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6. Usability of the international HAVNet hepatitis A virus database for geographical annotation, backtracing and outbreak detection
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Kroneman, Annelies, de Sousa, Rita, Verhoef, Linda, Koopmans, Marion P G, Vennema, Harry, On Behalf Of The HAVNet Network, and Virology
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0301 basic medicine ,Genotype ,Epidemiology ,030106 microbiology ,Disease Outbreaks ,Database ,03 medical and health sciences ,Annotation ,SDG 3 - Good Health and Well-being ,Virology ,Hepatitis A Virus ,Humans ,Cluster Analysis ,Phylogeny ,Infecções Sistémicas e Zoonoses ,Descriptive statistics ,Geography ,business.industry ,Public Health, Environmental and Occupational Health ,Online database ,Outbreak ,Genetic data ,Usability ,Sequence Analysis, DNA ,Hepatitis A ,Hepatitis a virus ,Metadata ,Molecular Typing ,Phylogeography ,030104 developmental biology ,RNA, Viral ,Hepatitis A virus ,business ,Cartography - Abstract
Background HAVNet is an international laboratory network sharing sequences and corresponding metadata on hepatitis A virus in an online database. Aim: We give an overview of the epidemiological and genetic data and assess the usability of the present dataset for geographical annotation, backtracing and outbreak detection. Methods: A descriptive analysis was performed on the timeliness, completeness, epidemiological data and geographic coverage of the dataset. Length and genomic region of the sequences were reviewed as well as the numerical and geographical distribution of the genotypes. The geographical signal in the sequences was assessed based on a short common nt stretch using a 100% identity analysis. Results: The 9,211 reports were heterogeneous for completeness and timeliness, and for length and genomic region of the sequences. Some parts of the world were not represented by the sequences. Geographical differences in prevalence of HAV genotypes described previously could be confirmed with this dataset and for a third (1,075/3,124) of the included sequences, 100% identity of the short common sequence coincided with an identical country of origin. Conclusion: Analysis of a subset of short, shared sequences indicates that a geographical annotation on the level of individual countries is possible with the HAVNet data. If the current incompleteness and heterogeneity of the data can be improved on, HAVNet could become very useful as a worldwide reference set for geographical annotation and for backtracing and outbreak detection.
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- 2018
7. HEVnet: A one health, collaborative, interdisciplinary network and sequence data repository for enhanced hepatitis e virus molecular typing, characterisation and epidemiological investigations
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Mulder, Annemieke Christine, Kroneman, Annelies, Franz, Eelco, Vennema, Harry, Tulen, Anna D., Takkinen, Johanna, Hofhuis, Agnetha, Adlhoch, Cornelia, Aberle, Stephan, Subissi, Lorenzo, Suin, Vanessa, Midgley, Sofie, Kuznetsova, Tatiana, Izopet, Jacques, Pavio, Nicole, Baechlein, Christine, Baylisa, Sally A., Corman, Victor M., Fabera, Mirko, Johne, Reimar, Kamp, Christel, Wenzel, Juergen J., Coughlan, Suzie, Di Bartolo, Ilaria, Bruni, Roberto, Ciccaglionea, Anna Rita, Garbuglia, Anna Rosa, Suffredini, Elisabetta, Boxman, Ingeborg, Hogema, Boris, van der Poel, Wim, Zaaijera, Hans, de Sousaa, Rita, Velebit, Branko, Avellóna, Ana, Buti, Maria, Girones, Rosina, Quer, Josep, Widén, Frederik, Norder, Heléne, Nyström, Kristina, Bachofen, Claudia, Sahli, Roland, Ijaza, Samreen, Treagus, Samantha, Kulka, Michael, Rizzi, Valentina, University of Zurich, and Hofhuis, Agnetha
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0301 basic medicine ,food-borne infections ,Swine ,Epidemiology ,genotype ,medicine.disease_cause ,Hepatitis E virus ,Zoonoses ,database ,Swine Diseases ,Reverse Transcriptase Polymerase Chain Reaction ,Transmission (medicine) ,Incidence (epidemiology) ,Zoonosis ,Hepatitis E ,zoonotic infections ,Virology & Molecular Biology ,Europe ,One Health ,Perspective ,RNA, Viral ,10244 Institute of Virology ,medicine.medical_specialty ,Meat ,viral infections ,030106 microbiology ,borne infections ,hepatitis E virus ,Biology ,03 medical and health sciences ,Virology ,Environmental health ,medicine ,Animals ,Humans ,Life Science ,HEVnet ,food ,Public health ,molecular typing ,Public Health, Environmental and Occupational Health ,2739 Public Health, Environmental and Occupational Health ,medicine.disease ,Virologie & Moleculaire Biologie ,030104 developmental biology ,HEV ,2406 Virology ,570 Life sciences ,biology ,hepatitis E ,2713 Epidemiology - Abstract
Hepatitis E virus (HEV) is a common cause of acute hepatitis worldwide. In Europe, HEV is a zoonosis transmitted via contaminated pork meat or other pork food products. Genotype 3 is the most prevalent HEV type in the animal reservoir, as well as in humans. Despite an increased incidence of hepatitis E across Europe, much remains unknown about its spread, sources and transmission routes. A One Health approach is crucial to better understand the (molecular) epidemiology of HEV. HEVnet was established in April 2017 as a network and database for sharing sequences and accompanying metadata collected from human, animal, food and environmental sources. HEVnet members working in the public health, veterinary health, food, environmental and blood safety sectors have submitted 1,615 HEV sequences from nine countries as at January 2019. Most are from humans (89%), and sequences of animal (5%), food (6%) or environmental (0.3%) origin are rare. Metadata for human sequences capture mostly sex (93%), year of birth (92%) and sampling (100%); data on region of sampling (37%) and clinical information (hospitalisation 27%, symptoms 20% or mortality 8%) are limited. HEVnet aims to expand into a global network capable of performing cross-sectoral and supranational studies, with a joint repository of molecular and epidemiological data on HEV.
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- 2019
8. Use of Norovirus Genotype Profiles to Differentiate Origins of Foodborne Outbreaks
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Verhoef, Linda, Vennema, Harry, van Pelt, Wilfrid, Lees, David, Boshuizen, Hendriek, Henshilwood, Kathleen, Koopmans, Marion, Böttiger, B., Mølbak, K., Johnsen, C., von Bonsdorff, K. H., Maunula, L., Kuusi, M., Pothier, P., Balay, K., Kaplon, J., Belliot, G., le Guyader, S., Schreier, E., Stark, K., Koch, J., Höhne, M., Szücs, G., Reuter, G., Krisztalovics, K., Lynch, M., Foley, B., McKeown, P., Coughlan, S., Duizer, E., Kroneman, A., van Duynhoven, Y., Vainio, K., Nygard, K., Kapperud, G., Poljsak-Prijatelj, M., Barlic-Maganja, D., Grom, A. Hocevar, Ruggeri, F., di Bartolo, I., Bosch, A., Dominguez, A., Buesa, J., Fauquier, A. Sanchez, Hernández-Pezzi, G., Hedlund, K. O., Andersson, Y., Thorhagen, M., Lysén, M., Hjertqvist, M., Virology, Clinical Chemistry, Erasmus MC other, and Gastroenterology & Hepatology
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Microbiology (medical) ,Veterinary medicine ,Genes, Viral ,Food Handling ,viruses ,genotype ,lcsh:Medicine ,Biology ,medicine.disease_cause ,infectious diseases ,Disease Outbreaks ,lcsh:Infectious and parasitic diseases ,Foodborne Diseases ,Feces ,SDG 3 - Good Health and Well-being ,Genotype ,medicine ,Animals ,Humans ,Shellfish Poisoning ,lcsh:RC109-216 ,Caliciviridae Infections ,Human feces ,Molecular epidemiology ,Transmission (medicine) ,Research ,food ,Norovirus ,lcsh:R ,transmission ,Outbreak ,Virology ,Genotype frequency ,Bivalvia ,Gastroenteritis ,outbreaks ,correlation ,surveillance ,epidemiology ,Food contaminant - Abstract
Detection should enable containment of viral foodborne infections., Because secondary transmission masks the connection between sources and outbreaks, estimating the proportion of foodborne norovirus infections is difficult. We studied whether norovirus genotype frequency distributions (genotype profiles) can enhance detection of the sources of foodborne outbreaks. Control measures differ substantially; therefore, differentiating this transmission mode from person-borne or food handler–borne outbreaks is of public health interest. Comparison of bivalve mollusks collected during monitoring (n = 295) and outbreak surveillance strains (n = 2,858) showed 2 distinguishable genotype profiles in 1) human feces and 2) source-contaminated food and bivalve mollusks; genotypes I.2 and I.4 were more frequently detected in foodborne outbreaks. Overall, ≈21% of all outbreaks were foodborne; further analysis showed that 25% of the outbreaks reported as food handler–associated were probably caused by source contamination of the food.
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- 2010
9. In-season and out-of-season variation of rotavirus genotype distribution and age of infection across 12 European countries before the introduction of routine vaccination, 2007/08 to 2012/13
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Hungerford, D., Vivancos, R., Read, J. M., Pitzer, V. E., Cunliffe, N., French, N., Iturrizagómara, M., Aberle, Stephan, Van Ranst, Marc, Matthijnssens, Jelle, Zeller, Mark, Mladenova, Zornitsa, Midgley, Sofie, Fischer, Thea Kølsen, Syriopoulou, Vassiliki P, Koukou, Dimitra M, Bányai, Krisztián, Dóró, Renáta, Kaplon, Jérôme, Pothier, Pierre, Maunula, Leena, Ruggeri, Franco Maria, Fiore, Lucia, Usonis, Vytautas, Ivaškevičienė, Inga, Vennema, Harry, Kroneman, Annelies, Poljsak-Prijatelj, Mateja, Steyer, Andrej, Buesa, Javier, Cilla, Gustavo, Montes, Milagroasa, Brytting, Mia, Schloss, Lottie, Marques, Andreas Mas, Allen, David James, and Nawaz, Sameena
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0301 basic medicine ,Diarrhea ,Rotavirus ,medicine.medical_specialty ,Genotype ,Epidemiology ,Logistic regression ,medicine.disease_cause ,Rotavirus Infections ,03 medical and health sciences ,Feces ,0302 clinical medicine ,Virology ,Journal Article ,medicine ,Humans ,030212 general & internal medicine ,Antigens, Viral ,business.industry ,Research Support, Non-U.S. Gov't ,Vaccination ,Public Health, Environmental and Occupational Health ,Rotavirus Vaccines ,Infant ,Odds ratio ,Confidence interval ,Hospitals ,3. Good health ,Gastroenteritis ,Europe ,Hospitalization ,030104 developmental biology ,Population Surveillance ,Immunology ,Vaccine-preventable diseases ,Female ,Seasons ,medicine.symptom ,business ,Demography - Abstract
The EuroRotaNet surveillance network has conducted rotavirus genotype surveillance since 2007 in 16 European countries. Using epidemiological and microbiological data from 39,786 genotyped rotavirus-positive specimens collected between September 2007 and August 2013, we assessed genotype distribution and age distribution of rotavirus gastroenteritis (RVGE) cases in and out of peak season in 12 countries which were yet to implement routine rotavirus vaccination. In multinomial multivariate logistic regression, adjusting for year, country and age, the odds of infection caused by genotype-constellation 2 DS-1-like stains (adjusted multinomial odds ratio (aM-OR) = 1.25; 95% confidence interval (CI): 1.13–1.37; p
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- 2015
10. Early occurrence of influenza A epidemics coincided with changes in occurrence of other respiratory virus infections.
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Asten, Liselotte, Bijkerk, Paul, Fanoy, Ewout, Ginkel, Annemarijn, Suijkerbuijk, Anita, Hoek, Wim, Meijer, Adam, and Vennema, Harry
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INFLUENZA A virus ,RESPIRATORY diseases ,RHINOVIRUSES ,COMPARATIVE studies ,EPIDEMIOLOGY - Abstract
Background Viral interaction in which outbreaks of influenza and other common respiratory viruses might affect each other has been postulated by several short studies. Regarding longer time periods, influenza epidemics occasionally occur very early in the season, as during the 2009 pandemic. Whether early occurrence of influenza epidemics impacts outbreaks of other common seasonal viruses is not clear. Objectives We investigated whether early occurrence of influenza outbreaks coincides with shifts in the occurrence of other common viruses, including both respiratory and non-respiratory viruses. Methods We investigated time trends of and the correlation between positive laboratory diagnoses of eight common viruses in the Netherlands over a 10-year time period (2003-2012): influenza viruses types A and B, respiratory syncytial virus (RSV), rhinovirus, coronavirus, norovirus, enterovirus, and rotavirus. We compared trends in viruses between early and late influenza seasons. Results Between 2003 and 2012, influenza B, RSV, and coronavirus showed shifts in their occurrence when influenza A epidemics occurred earlier than usual (before week 1). Although shifts were not always consistently of the same type, when influenza type A hit early, RSV outbreaks tended to be delayed, coronavirus outbreaks tended to be intensified, and influenza virus type B tended not to occur at all. Occurrence of rhinovirus, norovirus, rotavirus, and enterovirus did not change. Conclusion When influenza A epidemics occured early, timing of the epidemics of several respiratory winter viruses usually occurring close in time to influenza A was affected, while trends in rhinoviruses (occurring in autumn) and trends in enteral viruses were not. [ABSTRACT FROM AUTHOR]
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- 2016
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11. High Detection Rates of Enteropathogens in Asymptomatic Children Attending Day Care.
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Enserink, Remko, Scholts, Rianne, Bruijning-Verhagen, Patricia, Duizer, Erwin, Vennema, Harry, de Boer, Richard, Kortbeek, Titia, Roelfsema, Jeroen, Smit, Henriette, Kooistra-Smid, Mirjam, and van Pelt, Wilfrid
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PATHOGENIC microorganisms ,DIAGNOSTIC microbiology ,CHILD care services ,GASTROENTERITIS in children ,AGE factors in disease ,DISEASE prevalence ,SYMPTOMS - Abstract
Background: Gastroenteritis morbidity is high among children under the age of four, especially amongst those who attend day care. Objective: To determine the prevalence of a range of enteropathogens in the intestinal flora of children attending day care and to relate their occurrence with characteristics of the sampled child and the sampling season. Methods: We performed three years of enteropathogen surveillance in a network of 29 child day care centers in the Netherlands. The centers were instructed to take one fecal sample from ten randomly chosen children each month, regardless of gastrointestinal symptoms at time of sampling. All samples were analyzed for the molecular detection of 16 enteropathogenic bacteria, parasites and viruses by real-time multiplex PCR. Results: Enteropathogens were detected in 78.0% of the 5197 fecal samples. Of the total, 95.4% of samples were obtained from children who had no gastroenteritis symptoms at time of sampling. Bacterial enteropathogens were detected most often (most prevalent EPEC, 19.9%), followed by parasitic enteropathogens (most prevalent: D. fragilis, 22.1%) and viral enteropathogens (most prevalent: norovirus, 9.5%). 4.6% of samples related to children that experienced symptoms of gastroenteritis at time of sampling. Only rotavirus and norovirus were significantly associated with gastroenteritis among day care attendees. Conclusions: Our study indicates that asymptomatic infections with enteropathogens in day care attendees are not a rare event and that gastroenteritis caused by infections with these enteropathogens is only one expression of their presence. [ABSTRACT FROM AUTHOR]
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- 2014
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12. An Integrated Approach to Identifying International Foodborne Norovirus Outbreaks.
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Verhoef, Linda, Kouyos, Roger D., Vennema, Harry, Kroneman, Annelies, Siebenga, Joukje, van Pelt, Wilfrid, and Koopmans, Marion
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NOROVIRUSES ,RNA viruses ,VIRUSES ,EPIDEMIOLOGY ,RETROVIRUSES - Abstract
International foodborne norovirus outbreaks can be difficult to recognize when using standard outbreak investigation methods. In a novel approach, we provide step-wise selection criteria to identify clusters of outbreaks that may involve an internationally distributed common foodborne source. After computerized linking of epidemiologic data to aligned sequences, we retrospectively identified 100 individually reported outbreaks that potentially represented 14 international common source events in Europe during 1999-2008. Analysis of capsid sequences of outbreak strains (n = 1,456), showed that ≈7% of outbreaks reported to the Food-Borne Viruses in Europe database were part of an international event (range 2%-9%), compared with 0.4% identified through standard epidemiologic investigations. Our findings point to a critical gap in surveillance and suggest that international collaboration could have increased the number of recognized international foodborne outbreaks. Real-time exchange of combined epidemiologic and molecular data is needed to validate our findings through timely trace-backs of clustered outbreaks. [ABSTRACT FROM AUTHOR]
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- 2011
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13. Emergence of New Norovirus Variants on Spring Cruise Ships and Prediction of Winter Epidemics.
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Verhoef, Linda, Depoortere, Evelyn, Boxman, Ingeborg, Duizer, Erwin, Van Duynhoven, Yvonne, Harris, John, Johnsen, Christina, Kroneman, Annelies, Le Guyader, Soizick, Lim, Wilina, Maunula, Leena, Meldal, Hege, Ratcliff, Rod, Reuter, Gábor, Schreier, Eckart, Siebenga, Joukje, Vainio, Kirsti, Varela, Carmen, Vennema, Harry, and Koopmans, Marion
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NOROVIRUSES ,EPIDEMICS ,CRUISE ships ,CALICIVIRUSES ,EPIDEMIOLOGY ,COMMUNICABLE diseases - Abstract
In June 2006, reported outbreaks of norovirus on cruise ships suddenly increased; 43 outbreaks occurred on 13 vessels. All outbreaks investigated manifested person-to-person transmission. Detection of a point source was impossible because of limited investigation of initial outbreaks and data sharing. The most probable explanation for these outbreaks is increased norovirus activity in the community, which coincided with the emergence of 2 new GGII.4 variant strains in Europe and the Pacific. As in 2002, a new GGII.4 variant detected in the spring and summer corresponded with high norovirus activity in the subsequent winter. Because outbreaks on cruise ships are likely to occur when new variants circulate, an active reporting system could function as an early warning system. Internationally accepted guidelines are needed for reporting, investigating, and controlling norovirus illness on cruise ships in Europe. [ABSTRACT FROM AUTHOR]
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- 2008
14. Early Identification of Common-Source Foodborne Virus Outbreaks in Europe.
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Koopmans, Marion, Vennema, Harry, Heersma, Herre, van Strien, Elisabeth, van Duynhoven, Yvonne, Brown, David, Reacher, Marc, and Lopman, Ben
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FOODBORNE diseases , *VIRUSES , *COMMUNICABLE diseases , *DISEASE outbreaks , *EPIDEMIOLOGY - Abstract
Presents a study that examined the capabilities of European countries to early identify common-source of foodborne virus outbreaks. Methodology; Capability of laboratories to detect virus and genotype; Requested data fields for entries of viral sequences in the historic database.
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- 2003
15. Hepatitis A outbreaks.
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Severi, Ettore, Vennema, Harry, Takkinen, Johanna, Lopalco, Pier Luigi, and Coulombier, Denis
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HEPATITIS A , *DISEASE outbreaks , *NUCLEOTIDE sequence , *EPIDEMIOLOGY , *MICROBIOLOGY , *POMEGRANATE - Published
- 2015
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16. Polio and Measles Down the Drain: Environmental Enterovirus Surveillance in the Netherlands, 2005 to 2015.
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Benschop, Kimberley S. M., van der Avoort, Harrie G., Jusic, Edin, Vennema, Harry, van Binnendijk, Rob, and Duizer, Erwin
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MEASLES , *ENTEROVIRUSES , *MICROBIAL ecology , *EPIDEMIOLOGY , *DIAGNOSIS ,POLIO diagnosis - Abstract
Polioviruses (PVs) are members of the genus Enterovirus. In the Netherlands, the exclusion of PV circulation is based on clinical enterovirus (EV) surveillance (CEVS) of EV-positive cases and routine environmental EV surveillance (EEVS) conducted on sewage samples collected in the region of the Netherlands where vaccination coverage is low due to religious reasons. We compared the EEVS data to those of the CEVS to gain insight into the relevance of EEVS for poliovirus and nonpolio enterovirus surveillance. Following the polio outbreak in Syria, EEVS was performed at the primary refugee center in Ter Apel in the Netherlands, and data were compared to those of CEVS and EEVS. Furthermore, we assessed the feasibility of poliovirus detection by EEVS using measles virus detection in sewage during a measles outbreak as a proxy. Two Sabin-like PVs were found in routine EEVS, 11 Sabin-like PVs were detected in the CEVS, and one Sabin-like PV was found in the Ter Apel sewage. We observed significant differences between the three programs regarding which EVs were found. In 6 sewage samples collected during the measles outbreak in 2013, measles virus RNA was detected in regions where measles cases were identified. In conclusion, we detected PVs, nonpolio EVs, and measles virus in sewage and showed that environmental surveillance is useful for poliovirus detection in the Netherlands, where live oral poliovirus vaccine is not used and communities with lower vaccination coverage exist. EEVS led to the detection of EV types not seen in the CEVS, showing that EEVS is complementary to CEVS. IMPORTANCE We show that environmental enterovirus surveillance complements clinical enterovirus surveillance for poliovirus detection, or exclusion, and for nonpolio enterovirus surveillance. Even in the presence of adequate surveillance, only a very limited number of Sabin-like poliovirus strains were detected in a 10-year period, and no signs of transmission of oral polio vaccine (OPV) strains were found in a country using exclusively inactivated polio vaccine (IPV). Measles viruses can be detected during an outbreak in sewage samples collected and concentrated following procedures used for environmental enterovirus surveillance. [ABSTRACT FROM AUTHOR]
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- 2017
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17. Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020
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Alm E., Broberg E.K., Connor T., Hodcroft E.B., Komissarov A.B., Maurer-Stroh S., Melidou A., Neher R.A., O'Toole A., Pereyaslov D., Beerenwinkel N., Posada-Cespedes S., Jablonski K.P., Ferreira P.F., Topolsky I., Avsic-Zupanc T., Korva M., Poljak M., Zakotnik S., Zorec T.M., Bragstad K., Hungnes O., Stene-Johansen K., Reusken C., Meijer A., Vennema H., Ruiz-Roldan L., Bracho M.A., Garcia-Gonzalez N., Chiner-Oms A., Cancino-Munoz I., Comas I., Goig G.A., Torres-Puente M., Lopez M.G., Martinez-Priego L., D'Auria G., Ruiz-Hueso P., Ferrus-Abad L., de Marco G., Galan-Vendrell I., Carbo-Ramirez S., Ruiz-Rodriguez P., Coscolla M., Polackova K., Kramna L., Cinek O., Richter J., Krashias G., Tryfonos C., Bashiardes S., Koptides D., Christodoulou C., Bartolini B., Gruber C.E., Di Caro A., Castilletti C., Stefani F., Rimoldi S.G., Romeri F., Salerno F., Polesello S., Nagy A., Jirincova H., Vecerova J., Novakova L., Cordey S., Murtskhvaladze M., Kotaria N., Schar T., Beisel C., Vugrek O., Rokic F., Trgovec-Greif L., Jurak I., Rukavina T., Sucic N., Schonning K., Karst S.M., Kirkegaard R.H., Michaelsen T.Y., Sorensen E.A., Knutson S., Brandt J., Le-Quy V., Sorensen T., Petersen C., Pedersen M.S., Larsen S.L., Skov M.N., Rasmussen M., Fonager J., Fomsgaard A., Maksyutov R.A., Gavrilova E.V., Pyankov O.V., Bodnev S.A., Tregubchak T.V., Shvalov A.N., Antonets D.V., Resende P.C., Goya S., Perrin A., Lee R.T., Yadahalli S., Han A.X., Russell C.A., Schmutz S., Zaheri M., Kufner V., Huber M., Trkola A., Antwerpen M., Walter M.C., van der Werf S., Gambaro F., Behillil S., Enouf V., Donati F., Ustinova M., Rovite V., Klovins J., Savicka O., Wienecke-Baldacchino A.K., Ragimbeau C., Fournier G., Mossong J., Aberle S.W., Haukland M., Enkirch T., Advani A., Karlberg M.L., Lindsjo O.K., Broddesson S., Slavikova M., Lickova M., Klempa B., Staronova E., Ticha E., Szemes T., Rusnakova D., Stadler T., Quer J., Anton A., Andres C., Pinana M., Garcia-Cehic D., Pumarola T., Izopet J., Gioula G., Exindari M., Papa A., Chatzidimitriou D., Metallidis S., Pappa S., Macek M., Geryk J., Broz P., Briksi A., Hubacek P., Drevinek P., Zajac M., Kvapil P., Holub M., Kvapilova K., Novotny A., Kasny M., Klempt P., Vapalahti O., Smura T., Sironen T., Selhorst P., Anthony C., Arien K., Simon-Loriere E., Rabalski L., Bienkowska-Szewczyk K., Borges V., Isidro J., Gomes J.P., Guiomar R., Pechirra P., Costa I., Duarte S., Vieira L., Pyrc K., Zuckerman N.S., Turdikulova S., Abdullaev A., Dalimova D., Abdurakhimov A., Tagliabracci A., Alessandrini F., Melchionda F., Onofri V., Turchi C., Bagnarelli P., Menzo S., Caucci S., Di Sante L., Popa A., Genger J.-W., Agerer B., Lercher A., Endler L., Smyth M., Penz T., Schuster M., Senekowitsch M., Laine J., Bock C., Bergthaler A., Shevtsov A., Kalendar R., Ramanculov Y., Graf A., Muenchhoff M., Keppler O.T., Krebs S., Blum H., Marcello A., Licastro D., D'Agaro P., Laubscher F., Vidanovic D., Tesovic B., Volkening J., Clementi N., Mancini N., Rupnik M., Mahnic A., Walker A., Houwaart T., Wienemann T., Vasconcelos M.K., Strelow D., Jensen B.-E.O., Senff T., Hulse L., Adams O., Andree M., Hauka S., Feldt T., Keitel V., Kindgen-Milles D., Timm J., Pfeffer K., Dilthey A.T., Moore C., Ozdarendeli A., Pavel S.T.I., Yetiskin H., Aydin G., Holyavkin C., Uygut M.A., Cevik C., Shchetinin A., Gushchin V., Dinler-Doganay G., Doganay L., Kizilboga-Akgun T., Karacan I., Pancer K., Maes P., Marti-Carreras J., Wawina-Bokalanga T., Vanmechelen B., Thurmer A., Wedde M., Durrwald R., von Kleist M., Drechsel O., Wolff T., Fuchs S., Kmiecinski R., Michel J., Nitsche A., Casas I., Caballero M.I., Zaballos A., Jimenez P., Jimenez M., Fernandez S.M., Fernandez S.V., de la Plaza I.C., Fadeev A., Ivanova A., Sergeeva M., Stefanelli P., Estee Torok M., Hall G., da Silva Filipe A., Turtle L., Afifi S., McCluggage K., Beer R., Ledesma J., Maksimovic J., Spellman K., Hamilton W.L., Marchbank A., Southgate J.A., Underwood A., Taylor B., Yeats C., Abudahab K., Gemmell M.R., Eccles R., Lucaci A., Nelson C.A., Rainbow L., Whitehead M., Gregory R., Haldenby S., Paterson S., Hughes M.A., Curran M.D., Baker D., Tucker R., Green L.R., Feltwell T., Halstead F.D., Wyles M., Jahun A.S., Ahmad S.S.Y., Georgana I., Goodfellow I., Yakovleva A., Meredith L.W., Gavriil A., Awan A.R., Fisher C., Edgeworth J., Lynch J., Moore N., Williams R., Kidd S.P., Cortes N., Brunker K., McCrone J.T., Quick J., Duckworth N., Walsh S., Sloan T., Ludden C., George R.P., Eltringham G., Brown J.R., Aranday-Cortes E., Shepherd J.G., Hughes J., Li K.K., Williams T.C., Johnson N., Jesudason N., Mair D., Thomson E., Shah R., Parr Y.A., Carmichael S., Robertson D.L., Nomikou K., Broos A., Niebel M., Smollett K., Tong L., Miah S., Wittner A., Phillips N., Payne B., Dewar R., Holmes A., Bolt F., Price J.R., Mookerjee S., Sethi D.K., Potter W., Stanley R., Prakash R., Dervisevic S., Graham J.C., Nelson A., Smith D., Young G.R., Yew W.C., Todd J.A., Trebes A., Andersson M., Bull M., Watkins J., Birchley A., Gatica-Wilcox B., Gilbert L., Kumziene-Summerhayes S., Rey S., Chauhan A., Butcher E., Bicknell K., Elliott S., Glaysher S., Lackenby A., Bibby D., Platt S., Mohamed H., Machin N.W., Mbisa J.L., Evans J., Perry M., Pacchiarini N., Corden S., Adams A.G., Gaskin A., Coombs J., Graham L.J., Cottrell S., Morgan M., Gifford L., Kolyva A., Rudder S.J., Trotter A.J., Mather A.E., Aydin A., Page A.J., Kay G.L., de Oliveira Martins L., Yasir M., Alikhan N.-F., Thomson N.M., Gilroy R., Kingsley R.A., O'Grady J., Gutierrez A.V., Diaz M., Viet T.L., Tedim A.P., Adriaenssens E.M., Patrick Mcclure C., Sang F., Clark G., Howson-Wells H.C., Debebe J., Ball J., Chappell J., Khakh M., Carlile M., Loose M., Lister M.M., Holmes N., Tsoleridis T., Fleming V.M., Wright V., Smith W., Gallagher M.D., Parker M., Partridge D.G., Evans C., Baker P., Essex S., Liggett S., Keeley A.J., Bashton M., Rooke S., Dervisavic S., Meader E.J., Lopez C.E.B., Angyal A., Kristiansen M., Tutill H.J., Findlay J., Mestek-Boukhibar L., Forrest L., Dyal P., Williams R.J., Panchbhaya Y., Williams C.A., Roy S., Pandey S., Stockton J., Loman N.J., Poplawski R., Nicholls S., Rowe W.P.M., Khokhar F., Pinckert M.L., Hosmillo M., Chaudhry Y., Caller L.G., Davidson R.K., Griffith L., Rambaut A., Jackson B., Colquhoun R., Hill V., Nichols J., Asamaphan P., Darby A., Jackson K.A., Iturriza-Gomara M., Vamos E.E., Green A., Aanensen D., Bonsall D., Buck D., Macintyre-Cockett G., de Cesare M., Pybus O., Golubchik T., Scarlett G., Loveson K.F., Robson S.C., Beckett A., Lindsey B., Groves D.C., Parsons P.J., McHugh M.P., Barnes J.D., Manso C.F., Grammatopoulos D., Menger K.E., Harrison E., Gunson R., Peacock S.J., Gonzalez G., Carr M., Mihaela L., Popovici O., Brytting M., Bresner C., Fuller W., Workman T., Mentis A.F., Kossyvakis A., Karamitros T., Pogka V., Kalliaropoulos A., Horefti E., Kontou A., Martinez-Gonzalez B., Labropoulou V., Voulgari-Kokota A., Evangelidou M., Bizta P., Belimezi M., Lambrechts L., Doymaz M.Z., Yazici M.K., Cetin N.S., Karaaslan E., Kallio-Kokko H., Virtanen J., Suvanto M., Nguyen P.T., Ellonen P., Hannula S., Kangas H., Sreenu V.B., Burian K., Terhes G., Gombos K., Gyenesei A., Urban P., Herczeg R., Jakab F., Kemenesi G., Toth G.E., Somogyi B., Zana B., Zeghbib S., Kuczmog A., Foldes F., Lanszki Z., Madai M., Papp H., Pereszlenyi C.I., Babinszky G.C., Dudas G., Csoma E., Abou Tayoun A.N., Alsheikh-Ali A.A., Loney T., Nowotny N., Abdul-Wahab O., Gonzalez-Candelas F., Andersen M.H., Taylor S., MARTI CARRERAS, Joan, Vanmechelen, Bert, Wawina, Tony, Medical Microbiology and Infection Prevention, AII - Infectious diseases, WHO European Region Sequencing Lab, GISAID EpiCoV Grp, Erik, Alm, Eeva K, Broberg, Thomas, Connor, Emma B, Hodcroft, Andrey B, Komissarov, Sebastian, Maurer-Stroh, Angeliki, Melidou, Richard A, Neher, Áine, O’Toole, Dmitriy, Pereyaslov, WHO European Region sequencing laboratories and GISAID EpiCoV group (Niko Beerenwinkel, The, Posada-Céspedes, Susana, Philipp, Kim, Jablonski, Falé Ferreira, Pedro, Topolsky, Ivan, Avšičžupanc, Tatjana, Korva, Miša, Poljak, Mario, Zakotnik, Samo, Tomaž, Zorec, Mark, Bragstad, Karoline, Hungnes, Olav, Stene-Johansen, Kathrine, Reusken, Chantal, Meijer, Adam, Vennema, Harry, Ruiz-Roldán, Lidia, Alma Bracho, María, García-González, Neri, Chiner-Oms, Álvaro, Cancino-Muñoz, Irving, Comas, Iñaki, A Goig, Galo, Torres-Puente, Manuela, G López, Mariana, Martínez-Priego, Llúcia, D’Auria, Giuseppe, LoretoFerrús-Abad, de Marco, Griselda, Galan-Vendrell, Inmaculada, Carbó-Ramirez, Sandra, Ruíz-Hueso, Paula, Coscollá, Mireia, Polackova, Katerina, Kramna, Lenka, Cinek, Ondrej, Richter, Jan, Krashias, George, Tryfonos, Christina, Bashiardes, Stavro, Koptides, Dana, Christodoulou, Christina, Bartolini, Barbara, Em Gruber, Cesare, Di Caro, Antonino, Castilletti, Concetta, Stefani, Fabrizio, Giordana Rimoldi, Sara, Romeri, Francesca, Salerno, Franco, Polesello, Stefano, Nagy, Alexander, Jirincova, Helena, Vecerova, Jaromira, Novakova, Ludmila, Cordey, Samuel, Murtskhvaladze, Marine, Kotaria, Nato, Schär, Tobia, Beisel, Christian, Vugrek, Oliver, Rokić, Filip, Trgovecgreif, Lovro, Jurak, Igor, Rukavina, Tomislav, Sučić, Neven, Schønning, Kristian, M Karst, Søren, H Kirkegaard, Rasmu, Y Michaelsen, Thoma, Aa Sørensen, Emil, Knutson, Simon, Brandt, Jakob, Le-Quy, Vang, Sørensen, Trine, Petersen, Celine, Schou Pedersen, Martin, Løkkegaard Larsen, Sanne, Nielsine Skov, Marianne, Rasmussen, Morten, Fonager, Jannik, Fomsgaard, Ander, Amirovich Maksyutov, Rinat, Vasil’Evna Gavrilova, Elena, Victorovich Pyankov, Oleg, Alexandrovich Bodnev, Sergey, Vladimirovna Tregubchak, Tatyana, Nikolayevich Shvalov, Alexander, Victorovich Antonets, Deni, Cristina Resende, Paola, Goya, Stephanie, Perrin, Amandine, Tc Lee, Raphael, Yadahalli, Shilpa, X Han, Alvin, A Russell, Colin, Schmutz, Stefan, Zaheri, Maryam, Kufner, Verena, Huber, Michael, Trkola, Alexandra, Antwerpen, Marku, C Walter, Mathia, van der Werf, Sylvie, Gambaro, Fabiana, Behillil, Sylvie, Enouf, Vincent, Donati, Flora, Ustinova, Monta, Rovite, Vita, Klovins, Jani, Savicka, Oksana, K Wienecke-Baldacchino, Anke, Ragimbeau, Catherine, Fournier, Guillaume, Mossong, Joël, W Aberle, Stephan, Haukland, Mattia, Enkirch, Theresa, Advani, Abdolreza, Lind Karlberg, Maria, Karlsson Lindsjö, Oskar, Broddesson, Sandra, Sláviková, Monika, Ličková, Martina, Klempa, Bori, Staroňová, Edita, Tichá, Elena, Szemes, Tomáš, Rusňáková, Diana, Stadler, Tanja, Quer, Josep, Anton, Andre, Andres, Cristina, Piñana, Maria, Garcia-Cehic, Damir, Pumarola, Toma, Izopet, Jacque, Gioula, Georgia, Exindari, Maria, Papa, Anna, Chatzidimitriou, Dimitrio, Metallidis, Symeon, Pappa, Stella, Macek Jr, Milan, Geryk, Jan, Brož, Petr, Briksí, Aleš, Hubáček, Petr, Dřevínek, Pavel, Zajac, Miroslav, Kvapil, Petr, Holub, Michal, Kvapilová, Kateřina, Novotný, Adam, Kašný, Martin, Klempt, Petr, Vapalahti, Olli, Smura, Teemu, Sironen, Tarja, Selhorst, Philippe, Anthony, Colin, Ariën, Kevin, Simon-Loriere, Etienne, Rabalski, Lukasz, Bienkowska-Szewczyk, Krystyna, Borges, Vítor, Isidro, Joana, Paulo Gomes, João, Guiomar, Raquel, Pechirra, Pedro, Costa, Inê, Duarte, Sílvia, Vieira, Luí, Pyrc, Krzysztof, S Zuckerman, Neta, Turdikulova, Shahlo, Abdullaev, Alisher, Dalimova, Dilbar, Abdurakhimov, Abror, Tagliabracci, Adriano, Alessandrini, Federica, Melchionda, Filomena, Onofri, Valerio, Turchi, Chiara, Bagnarelli, Patrizia, Menzo, Stefano, Caucci, Sara, Di Sante, Laura, Popa, Alexandra, Genger, Jakob-Wendelin, Agerer, Benedikt, Lercher, Alexander, Endler, Luka, Smyth, Mark, Penz, Thoma, Schuster, Michael, Senekowitsch, Martin, Laine, Jan, Bock, Christoph, Bergthaler, Andrea, Shevtsov, Alexandr, Kalendar, Ruslan, Ramanculov, Yerlan, Graf, Alexander, Muenchhoff, Maximilian, T Keppler, Oliver, Krebs, Stefan, Blum, Helmut, Marcello, Alessandro, Licastro, Danilo, D’Agaro, Pierlanfranco, Laubscher, Florian, Vidanovic, Dejan, Tesovic, Bojana, Volkening, Jeremy, Clementi, Nicola, Mancini, Nicasio, Rupnik, Maja, Mahnic, Aleksander, Walker, Andrea, Houwaart, Torsten, Wienemann, Tobia, Kohns Vasconcelos, Malte, Strelow, Daniel, Ole Jensen, Björn-Erik, Senff, Tina, Hülse, Lisanna, Adams, Ortwin, Andree, Marcel, Hauka, Sandra, Feldt, Torsten, Keitel, Verena, Kindgen-Milles, Detlef, Timm, Jörg, Pfeffer, Klau, T Dilthey, Alexander, Moore, Catherine, Ozdarendeli, Aykut, Terkis Islam Pavel, Shaikh, Yetiskin, Hazel, Aydin, Gunsu, Holyavkin, Can, Ali Uygut, Muhammet, Cevik, Ceren, Shchetinin, Alexey, Gushchin, Vladimir, Dinler-Doganay, Gizem, Doganay, Levent, Kizilboga-Akgun, Tugba, Karacan, Ilker, Pancer, Katarzyna, Maes, Piet, Martí-Carreras, Joan, Wawina-Bokalanga, Tony, Thürmer, Andrea, Wedde, Marianne, Dürrwald, Ralf, Von Kleist, Max, Drechsel, Oliver, Wolff, Thorsten, Fuchs, Stephan, Kmiecinski, Rene, Michel, Janine, Nitsche, Andrea, Casas, Inmaculada, Iglesias Caballero, María, Zaballos, Ángel, Jiménez, Pilar, Jiménez, Mercede, Monzón Fernández, Sara, Varona Fernández, Sarai, Cuesta De La Plaza, Isabel, Fadeev, Artem, Ivanova, Anna, Sergeeva, Mariia, Stefanelli, Paola, Estee Torok, M, Hall, Grant, da Silva Filipe, Ana, Turtle, Lance, Afifi, Safiah, Mccluggage, Kathryn, Beer, Robert, Ledesma, Juan, Maksimovic, Joshua, Spellman, Karla, L Hamilton, William, Marchbank, Angela, Alexander Southgate, Joel, Underwood, Anthony, Taylor, Ben, Yeats, Corin, Abudahab, Khalil, R Gemmell, Matthew, Eccles, Richard, Lucaci, Anita, Abigail Nelson, Charlotte, Rainbow, Lucille, Whitehead, Mark, Gregory, Richard, Haldenby, Sam, Paterson, Steve, A Hughes, Margaret, D Curran, Martin, Baker, David, Tucker, Rachel, R Green, Luke, Feltwell, Theresa, D Halstead, Fenella, Wyles, Matthew, S Jahun, Aminu, Y Ahmad, Shazaad S, Georgana, Iliana, Goodfellow, Ian, Yakovleva, Anna, W Meredith, Luke, Gavriil, Artemi, Raza Awan, Ali, Fisher, Chloe, Jonathan, European Centre for Disease Prevention and Control [Stockholm, Sweden] (ECDC), Cardiff University, Public Health Wales [Cardiff, Royaume uni], University of Basel (Unibas), Research Institute of Influenza, St. Petersburg, Russia, Agency for science, technology and research [Singapore] (A*STAR), National University of Singapore (NUS), University of Edinburgh, WHO Regional Office for Europe [Copenhagen], We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GISAID’s EpiCoV Database used in the phylogenetic analysis. We gratefully acknowledge all the staff working with sample collection, sample preparation, sequencing, data analysis and data sharing in all laboratories in the WHO European Region for making this work possible, The WHO European Region sequencing laboratories and GISAID EpiCoV group*: Niko Beerenwinkel, Susana Posada-Céspedes, Kim Philipp Jablonski, Pedro Falé Ferreira, Ivan Topolsky, Tatjana Avšič-Županc, Miša Korva, Mario Poljak, Samo Zakotnik, Tomaž Mark Zorec, Karoline Bragstad, Olav Hungnes, Kathrine Stene-Johansen, Chantal Reusken, Adam Meijer, Harry Vennema, Lidia Ruiz-Roldán, María Alma Bracho, Neris García-González, Álvaro Chiner-Oms, Irving Cancino-Muñoz, Iñaki Comas, Galo A Goig, Manuela Torres-Puente, Mariana G López, Llúcia Martínez-Priego, Giuseppe D'Auria, Paula Ruíz-Hueso, Loreto Ferrús-Abad, Griselda de Marco, Inmaculada Galan-Vendrell, Sandra Carbó-Ramirez, Paula Ruiz-Rodriguez, Mireia Coscollá, Katerina Polackova, Lenka Kramna, Ondrej Cinek, Jan Richter, George Krashias, Christina Tryfonos, Stavros Bashiardes, Dana Koptides, Christina Christodoulou, Barbara Bartolini, Cesare Em Gruber, Antonino Di Caro, Concetta Castilletti, Fabrizio Stefani, Sara Giordana Rimoldi, Francesca Romeri, Franco Salerno, Stefano Polesello, Alexander Nagy, Helena Jirincova, Jaromira Vecerova, Ludmila Novakova, Samuel Cordey, Marine Murtskhvaladze, Nato Kotaria, Tobias Schär, Christian Beisel, Oliver Vugrek, Filip Rokić, Lovro Trgovec-Greif, Igor Jurak, Tomislav Rukavina, Neven Sučić, Kristian Schønning, Søren M Karst, Rasmus H Kirkegaard, Thomas Y Michaelsen, Emil Aa Sørensen, Simon Knutson, Jakob Brandt, Vang Le-Quy, Trine Sørensen, Celine Petersen, Martin Schou Pedersen, Sanne Løkkegaard Larsen, Marianne Nielsine Skov, Morten Rasmussen, Jannik Fonager, Anders Fomsgaard, Rinat Amirovich Maksyutov, Elena Vasil'Evna Gavrilova, Oleg Victorovich Pyankov, Sergey Alexandrovich Bodnev, Tatyana Vladimirovna Tregubchak, Alexander Nikolayevich Shvalov, Denis Victorovich Antonets, Paola Cristina Resende, Stephanie Goya, Amandine Perrin, Raphael Tc Lee, Shilpa Yadahalli, Alvin X Han, Colin A Russell, Stefan Schmutz, Maryam Zaheri, Verena Kufner, Michael Huber, Alexandra Trkola, Markus Antwerpen, Mathias C Walter, Sylvie van der Werf, Fabiana Gambaro, Sylvie Behillil, Vincent Enouf, Flora Donati, Monta Ustinova, Vita Rovite, Janis Klovins, Oksana Savicka, Anke K Wienecke-Baldacchino, Catherine Ragimbeau, Guillaume Fournier, Joël Mossong, Stephan W Aberle, Mattias Haukland, Theresa Enkirch, Abdolreza Advani, Maria Lind Karlberg, Oskar Karlsson Lindsjö, Sandra Broddesson, Monika Sláviková, Martina Ličková, Boris Klempa, Edita Staroňová, Elena Tichá, Tomáš Szemes, Diana Rusňáková, Tanja Stadler, Josep Quer, Andres Anton, Cristina Andres, Maria Piñana, Damir Garcia-Cehic, Tomas Pumarola, Jacques Izopet, Georgia Gioula, Maria Exindari, Anna Papa, Dimitrios Chatzidimitriou, Symeon Metallidis, Stella Pappa, Milan Macek Jr, Jan Geryk, Petr Brož, Aleš Briksí, Petr Hubáček, Pavel Dřevínek, Miroslav Zajac, Petr Kvapil, Michal Holub, Kateřina Kvapilová, Adam Novotný, Martin Kašný, Petr Klempt, Olli Vapalahti, Teemu Smura, Tarja Sironen, Philippe Selhorst, Colin Anthony, Kevin Ariën, Etienne Simon-Loriere, Lukasz Rabalski, Krystyna Bienkowska-Szewczyk, Vítor Borges, Joana Isidro, João Paulo Gomes, Raquel Guiomar, Pedro Pechirra, Inês Costa, Sílvia Duarte, Luís Vieira, Krzysztof Pyrc, Neta S Zuckerman, Shahlo Turdikulova, Alisher Abdullaev, Dilbar Dalimova, Abror Abdurakhimov, Adriano Tagliabracci, Federica Alessandrini, Filomena Melchionda, Valerio Onofri, Chiara Turchi, Patrizia Bagnarelli, Stefano Menzo, Sara Caucci, Laura Di Sante, Alexandra Popa, Jakob-Wendelin Genger, Benedikt Agerer, Alexander Lercher, Lukas Endler, Mark Smyth, Thomas Penz, Michael Schuster, Martin Senekowitsch, Jan Laine, Christoph Bock, Andreas Bergthaler, Alexandr Shevtsov, Ruslan Kalendar, Yerlan Ramanculov, Alexander Graf, Maximilian Muenchhoff, Oliver T Keppler, Stefan Krebs, Helmut Blum, Alessandro Marcello, Danilo Licastro, Pierlanfranco D'Agaro, Florian Laubscher, Dejan Vidanovic, Bojana Tesovic, Jeremy Volkening, Nicola Clementi, Nicasio Mancini, Maja Rupnik, Aleksander Mahnic, Andreas Walker, Torsten Houwaart, Tobias Wienemann, Malte Kohns Vasconcelos, Daniel Strelow, Björn-Erik Ole Jensen, Tina Senff, Lisanna Hülse, Ortwin Adams, Marcel Andree, Sandra Hauka, Torsten Feldt, Verena Keitel, Detlef Kindgen-Milles, Jörg Timm, Klaus Pfeffer, Alexander T Dilthey, Catherine Moore, Aykut Ozdarendeli, Shaikh Terkis Islam Pavel, Hazel Yetiskin, Gunsu Aydin, Can Holyavkin, Muhammet Ali Uygut, Ceren Cevik, Alexey Shchetinin, Vladimir Gushchin, Gizem Dinler-Doganay, Levent Doganay, Tugba Kizilboga-Akgun, Ilker Karacan, Katarzyna Pancer, Piet Maes, Joan Martí-Carreras, Tony Wawina-Bokalanga, Bert Vanmechelen, Andrea Thürmer, Marianne Wedde, Ralf Dürrwald, Max Von Kleist, Oliver Drechsel, Thorsten Wolff, Stephan Fuchs, Rene Kmiecinski, Janine Michel, Andreas Nitsche, Inmaculada Casas, María Iglesias Caballero, Ángel Zaballos, Pilar Jiménez, Mercedes Jiménez, Sara Monzón Fernández, Sarai Varona Fernández, Isabel Cuesta De La Plaza, Artem Fadeev, Anna Ivanova, Mariia Sergeeva, Paola Stefanelli, M Estee Torok, Grant Hall, Ana da Silva Filipe, Lance Turtle, Safiah Afifi, Kathryn Mccluggage, Robert Beer, Juan Ledesma, Joshua Maksimovic, Karla Spellman, William L Hamilton, Angela Marchbank, Joel Alexander Southgate, Anthony Underwood, Ben Taylor, Corin Yeats, Khalil Abudahab, Matthew R Gemmell, Richard Eccles, Anita Lucaci, Charlotte Abigail Nelson, Lucille Rainbow, Mark Whitehead, Richard Gregory, Sam Haldenby, Steve Paterson, Margaret A Hughes, Martin D Curran, David Baker, Rachel Tucker, Luke R Green, Theresa Feltwell, Fenella D Halstead, Matthew Wyles, Aminu S Jahun, Shazaad S Y Ahmad, Iliana Georgana, Ian Goodfellow, Anna Yakovleva, Luke W Meredith, Artemis Gavriil, Ali Raza Awan, Chloe Fisher, Jonathan Edgeworth, Jessica Lynch, Nathan Moore, Rebecca Williams, Stephen P Kidd, Nicholas Cortes, Kirstyn Brunker, John T Mccrone, Joshua Quick, Nichola Duckworth, Sarah Walsh, Tim Sloan, Catherine Ludden, Ryan P George, Gary Eltringham, Julianne R Brown, Elihu Aranday-Cortes, James G Shepherd, Joseph Hughes, Kathy K Li, Thomas C Williams, Natasha Johnson, Natasha Jesudason, Daniel Mair, Emma Thomson, Rajiv Shah, Yasmin A Parr, Stephen Carmichael, David L Robertson, Kyriaki Nomikou, Alice Broos, Marc Niebel, Katherine Smollett, Lily Tong, Shahjahan Miah, Anita Wittner, Nicole Phillips, Brendan Payne, Rebecca Dewar, Alison Holmes, Frances Bolt, James R Price, Siddharth Mookerjee, Dheeraj K Sethi, Will Potter, Rachael Stanley, Reenesh Prakash, Samir Dervisevic, Jonathan Clive Graham, Andrew Nelson, Darren Smith, Gregory R Young, Wen Chyin Yew, John A Todd, Amy Trebes, Monique Andersson, Matthew Bull, Joanne Watkins, Alec Birchley, Bree Gatica-Wilcox, Lauren Gilbert, Sara Kumžiene-Summerhayes, Sara Rey, Anoop Chauhan, 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H., Taylor, S., European Centre for Disease Prevention and Control (ECDC), Public Health Wales Microbiology Cardiff, Faculty of Agriculture and Forestry, Department of Agricultural Sciences, and Institute of Biotechnology
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Infecções Respiratórias ,0301 basic medicine ,MESH: Coronavirus Infections ,Epidemiology ,[SDV]Life Sciences [q-bio] ,Distribution (economics) ,Wastewater ,MESH: Base Sequence ,Severe Acute Respiratory Syndrome ,MESH: World Health Organization ,Pandemic ,MESH: Coronavirus ,MESH: COVID-19 ,Sequencing ,Viral ,Clade ,Nomenclature ,Genome ,biology ,COVID-19 ,Europe ,NGS ,SARS-CoV-2 ,WGS ,nomenclature ,sequencing ,Base Sequence ,Betacoronavirus ,Coronavirus ,Coronavirus Infections ,Genome, Viral ,Humans ,Phylogeography ,Pneumonia, Viral ,RNA, Viral ,RNA-Dependent RNA Polymerase ,Spatio-Temporal Analysis ,World Health Organization ,Pandemics ,C500 ,European region ,3. Good health ,Geography ,MESH: Phylogeography ,MESH: RNA-Dependent RNA Polymerase ,MESH: RNA, Viral ,MESH: Betacoronavirus ,Spatio-Temporal Analysi ,MESH: Genome, Viral ,Cartography ,Human ,Bioquímica ,MESH: Pandemics ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Coronaviru ,030106 microbiology ,03 medical and health sciences ,MESH: Spatio-Temporal Analysis ,MESH: Severe Acute Respiratory Syndrome ,Virology ,MESH: SARS-CoV-2 ,Whole genome sequencing ,MESH: Humans ,Whole Genome Sequencing ,Betacoronaviru ,Coronavirus Infection ,business.industry ,Public Health, Environmental and Occupational Health ,Pneumonia ,biology.organism_classification ,B900 ,030104 developmental biology ,MESH: Pneumonia, Viral ,RNA ,SARS_CoV-2 ,3111 Biomedicine ,MESH: Europe ,Human medicine ,business - Abstract
8 páginas, 3 figuras, We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2., We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GISAID’s EpiCoV Database used in the phylogenetic analysis. We gratefully acknowledge all the staff working with sample collection, sample preparation, sequencing, data analysis and data sharing in all laboratories in the WHO European Region for making this work possible.
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