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2. Use of passive samplers as sewage surveillance tool to monitor a hepatitis A outbreak at a school in Amsterdam, the Netherlands, Oct 2022 – March 2023

Author

de Jong, Maarten, primary, Loeff, Maarten F. Schim van der, additional, Schilperoort, Rémy, additional, Vennema, Harry, additional, Weijden, Charlie van der, additional, Langeveld, Jeroen, additional, Welkers, Matthijs, additional, Prins, Maria, additional, Husman, Ana Maria Roda, additional, Fanoy, Ewout, additional, and Medema, Gertjan, additional

Published
2024
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3. Detection of Norovirus Variant GII.4 Hong Kong in Asia and Europe, 2017-2019

Author

Chan, Martin Chi-Wai, Roy, Sunando, Bonifacio, Joseph, Zhang, Lin-Yao, Chhabra, Preeti, Chan, Jenny C.M., Celma, Cristina, Igoy, Mary Ann, Lau, Sin-Leung, Mohammad, Kirran N., Vinje, Jan, Vennema, Harry, Breuer, Judith, Koopmans, Marion, and de Graaf, Miranda

Subjects
Norovirus -- Identification and classification -- Varieties -- Distribution, Company distribution practices, Health
Abstract

Noroviruses are a genetically diverse group of RNA viruses found in a plethora of terrestrial, aerial, and aquatic mammalian species, including humans, pigs, cows, sheep, rats, bats, sea lions, and [...]

Published
2021
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6. Molecular surveillance of norovirus, 2005–16: an epidemiological analysis of data collected from the NoroNet network

Author

van Beek, Janko, de Graaf, Miranda, Al-Hello, Haider, Allen, David J, Ambert-Balay, Katia, Botteldoorn, Nadine, Brytting, Mia, Buesa, Javier, Cabrerizo, Maria, Chan, Martin, Cloak, Fiona, Di Bartolo, Ilaria, Guix, Susana, Hewitt, Joanne, Iritani, Nobuhiro, Jin, Miao, Johne, Reimar, Lederer, Ingeborg, Mans, Janet, Martella, Vito, Maunula, Leena, McAllister, Georgina, Niendorf, Sandra, Niesters, Hubert G, Podkolzin, Alexander T, Poljsak-Prijatelj, Mateja, Rasmussen, Lasse Dam, Reuter, Gábor, Tuite, Gráinne, Kroneman, Annelies, Vennema, Harry, and Koopmans, Marion P G

Published
2018
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8. Higher risk of SARS-CoV-2 Omicron BA.4/5 infection than of BA.2 infection after previous BA.1 infection, the Netherlands, 2 May to 24 July 2022

Author

Andeweg, Stijn P, primary, de Gier, Brechje, additional, Vennema, Harry, additional, van Walle, Ivo, additional, van Maarseveen, Noortje, additional, Kusters, Nina E, additional, de Melker, Hester E, additional, Hahné, Susan JM, additional, van den Hof, Susan, additional, Eggink, Dirk, additional, and Knol, Mirjam J, additional

Published
2023
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9. Mpox outbreak in the Netherlands, 2022: public health response, characteristics of the first 1,000 cases and protection of the first-generation smallpox vaccine

Author

van Ewijk, Catharina E., Miura, Fuminari, van Rijckevorsel, Gini, de Vries, Henry Jc, Welkers, Matthijs Ra, van den Berg, Oda E., Friesema, Ingrid Hm, van den Berg, Patrick R., Dalhuisen, Thomas, Wallinga, Jacco, Brandwagt, Diederik, van Cleef, Brigitte Agl, Vennema, Harry, Voordouw, Bettie, Koopmans, Marion, van der Eijk, Annemiek A., Swaan, Corien M., Te Wierik, Margreet Jm, Leenstra, Tjalling, Op de Coul, Eline, Franz, Eelco, and Virology

Subjects
SDG 3 - Good Health and Well-being, Mpox, outbreak, the Netherlands, MSM, zoonoses
Abstract

In early May 2022, a global outbreak of mpox started among persons without travel history to regions known to be enzootic for monkeypox virus (MPXV). On 8 August 2022, the Netherlands reported its 1,000th mpox case, representing a cumulative incidence of 55 per million population, one of the highest cumulative incidences worldwide. We describe characteristics of the first 1,000 mpox cases in the Netherlands, reported between 20 May and 8 August 2022, within the context of the public health response. These cases were predominantly men who have sex with men aged 31-45 years. The vast majority of infections were acquired through sexual contact with casual partners in private or recreational settings including LGBTQIA+ venues in the Netherlands. This indicates that, although some larger upsurges occurred from point-source and/or travel-related events, the outbreak was mainly characterised by sustained transmission within the Netherlands. In addition, we estimated the protective effect of first-generation smallpox vaccine against moderate/severe mpox and found a vaccine effectiveness of 58% (95% CI: 17-78%), suggesting moderate protection against moderate/severe mpox symptoms on top of any possible protection by this vaccine against MPXV infection and disease. Communication with and supporting the at-risk population in following mitigation measures remains essential.

Published
2023

11. Global spread of norovirus GII.17 Kawasaki 308, 2014-2016

Author

Chan, Martin C.W., Hu, Yunwen, Chen, Haili, Podkolzin, Alexander T., Zaytseva, Ekaterina V., Komano, Jun, Sakon, Naomi, Poovorawan, Yong, Vongpunsawad, Sompong, Thanusuwannasak, Thanundorn, Hewitt, Joanne, Croucher, Dawn, Collins, Nikail, Vinje, Jan, Pang, Xiaoli L., Lee, Bonita E., de Graaf, Miranda, van Beek, Janko, Vennema, Harry, Koopmans, Marion P.G., Niendorf, Sandra, Poljsak-Prijatelj, Mateja, Steyer, Andrej, White, Peter A., Lun, Jennifer H., Mans, Janet, Hung, Tin -Nok, Kwok, Kirsty, Cheung, Kelton, Lee, Nelson, and Chan, Paul K.S.

Subjects
B cells -- Health aspects -- Analysis, Gastroenteritis -- Genetic aspects -- Health aspects -- Analysis, Health
Abstract

Norovirus infections are a leading cause of acute gastroenteritis worldwide in persons of all age groups. Despite the broad genetic diversity, norovirus GII.4 has predominated during the past 20 years [...]

Published
2017
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14. Higher risk of SARS-CoV-2 Omicron BA.4/5 infection than of BA.2 infection after previous BA.1 infection, the Netherlands, 2 May to 24 July 2022

Author

Andeweg, Stijn P., primary, de Gier, Brechje, additional, Vennema, Harry, additional, van Walle, Ivo, additional, van Maarseveen, Noortje, additional, Kusters, Nina E., additional, de Melker, Hester E., additional, Hahné, Susan J.M., additional, van den Hof, Susan, additional, Eggink, Dirk, additional, and Knol, Mirjam J., additional

Published
2022
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15. Antigenic cartography using sera from sequence-confirmed SARS-CoV-2 variants of concern infections reveals antigenic divergence of Omicron

Author

van der Straten, Karlijn, primary, Guerra, Denise, additional, van Gils, Marit J., additional, Bontjer, Ilja, additional, Caniels, Tom G., additional, van Willigen, Hugo D.G., additional, Wynberg, Elke, additional, Poniman, Meliawati, additional, Burger, Judith A., additional, Bouhuijs, Joey H., additional, van Rijswijk, Jacqueline, additional, Olijhoek, Wouter, additional, Liesdek, Marinus H., additional, Lavell, A.H. Ayesha, additional, Appelman, Brent, additional, Sikkens, Jonne J., additional, Bomers, Marije K., additional, Han, Alvin X., additional, Nichols, Brooke E., additional, Prins, Maria, additional, Vennema, Harry, additional, Reusken, Chantal, additional, de Jong, Menno D., additional, de Bree, Godelieve J., additional, Russell, Colin A., additional, Eggink, Dirk, additional, and Sanders, Rogier W., additional

Published
2022
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18. SARS-CoV-2 outbreaks in secondary school settings in the Netherlands during fall 2020; silent circulation

Author

Jonker, Lotte, primary, Linde, Kimberly J, additional, de Hoog, Marieke LA, additional, Sprado, Robin, additional, Huisman, Robin, additional, Molenkamp, Richard, additional, Oude Munnink, Bas B, additional, Dohmen, Wietske, additional, Heederik, Dick JJ, additional, Eggink, Dirk, additional, Welkers, Matthijs RA, additional, Vennema, Harry, additional, Koopmans, Marion PG, additional, Fraaij, Pieter LA, additional, Wouters, Inge M, additional, and Bruijning-Verhagen, Patricia CJL, additional

Published
2022
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19. 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

Author

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

Subjects
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

20. Elevated risk of infection with SARS-CoV-2 Beta, Gamma, and Delta variants compared with Alpha variant in vaccinated individuals.

Author

Andeweg, Stijn P., Vennema, Harry, Veldhuijzen, Irene, Smorenburg, Naomi, Schmitz, Dennis, Zwagemaker, Florian, van Gageldonk-Lafeber, Arianne B., Hahné, Susan J. M., Reusken, Chantal, Knol, Mirjam J., and Eggink, Dirk

Subjects
SARS-CoV-2 Delta variant, SARS-CoV-2, VACCINE effectiveness, BREAKTHROUGH infections, VACCINATION
Abstract

The extent to which severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) break through infection- or vaccine-induced immunity is not well understood. We analyzed 28,578 sequenced SARS-CoV-2 samples from individuals with known immune status obtained through national community testing in the Netherlands from March to August 2021. We found evidence of an increased risk of infection by the Beta (B.1.351), Gamma (P.1), or Delta (B.1.617.2) variants compared with the Alpha (B.1.1.7) variant after vaccination. No clear differences were found between vaccines. However, the effect was larger in the first 14 to 59 days after complete vaccination compared with ≥60 days. In contrast to vaccine-induced immunity, there was no increased risk for reinfection with Beta, Gamma, or Delta variants relative to the Alpha variant in individuals with infection-induced immunity. Variants and vaccines: The emergence of SARS-CoV-2 variants has revealed that breakthrough infections can occur despite previous immunity caused by infection or vaccination. Andeweg et al. used SARS-CoV-2 sequence data collected during March to August 2021 through the national community testing program in the Netherlands to understand the relationship between immune status and breakthrough infection. They analyzed 28,578 samples and observed an increased risk of infection by the Beta (B.1.351), Gamma (P.1), or Delta (B.1.617.2) variants compared with the Alpha (B.1.1.7) variant after vaccination regardless of vaccine type. The risk of breakthrough infection with variants Beta, Gamma, or Delta was greatest 14 to 59 days after vaccination compared with >60 days, but no differences between variants were observed in unvaccinated individuals who had been previously infected with SARS-CoV-2. These findings highlight the effect viral variants have on vaccine efficacy. —CF [ABSTRACT FROM AUTHOR]

Published
2023
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22. 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

Author

Eggink, Dirk, primary, Andeweg, Stijn P, additional, Vennema, Harry, additional, van Maarseveen, Noortje, additional, Vermaas, Klaas, additional, Vlaemynck, Boris, additional, Schepers, Raf, additional, van Gageldonk-Lafeber, Arianne B, additional, van den Hof, Susan, additional, Reusken, Chantal BEM, additional, and Knol, Mirjam J, additional

Published
2022
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23. Mapping the antigenic diversification of SARS-CoV-2

Author

van der Straten, Karlijn, primary, Guerra, Denise, additional, van Gils, Marit J., additional, Bontjer, Ilja, additional, Caniels, Tom G., additional, van Willigen, Hugo D.G., additional, Wynberg, Elke, additional, Poniman, Meliawati, additional, Burger, Judith A., additional, Bouhuijs, Joey H., additional, van Rijswijk, Jacqueline, additional, Olijhoek, Wouter, additional, Liesdek, Marinus H., additional, Lavell, A. H. Ayesha, additional, Appelman, Brent, additional, Sikkens, Jonne J., additional, Bomers, Marije K., additional, Han, Alvin X., additional, Nichols, Brooke E., additional, Prins, Maria, additional, Vennema, Harry, additional, Reusken, Chantal, additional, de Jong, Menno D., additional, de Bree, Godelieve J., additional, Russell, Colin A., additional, Eggink, Dirk, additional, and Sanders, Rogier W., additional

Published
2022
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24. Tick-borne encephalitis virus in ticks and roe deer, the Netherlands

Author

Jahfari, Setareh, de Vries, Ankje, Rijks, Jolianne M., Van Gucht, Steven, Vennema, Harry, Sprong, Hein, and Rockx, Barry

Subjects
Tick-borne encephalitis -- Risk factors -- Research, Enzyme-linked immunosorbent assay -- Usage, European roe deer -- Physiological aspects, Health
Abstract

Tick-borne encephalitis virus (TBEV) can infect humans, causing febrile illness; neurologic complications include encephalitis (1). TBEV is transmitted through bites of infected ticks to many animals, including deer, which serve [...]

Published
2017
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25. Norovirus Illness Is a Global Problem: Emergence and Spread of Norovirus GII4. Variants, 2001-2007

Author

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

Published
2009
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28. Increased risk of infection with SARS-CoV-2 Omicron compared to Delta in vaccinated and previously infected individuals, the Netherlands, 22 November to 19 December 2021

Author

Eggink, Dirk, primary, Andeweg, Stijn P., additional, Vennema, Harry, additional, van Maarseveen, Noortje, additional, Vermaas, Klaas, additional, Vlaemynck, Boris, additional, Schepers, Raf, additional, van Gageldonk-Lafeber, Arianne B., additional, van den Hof, Susan, additional, Reusken, Chantal B.E.M., additional, and Knol, Mirjam J., additional

Published
2021
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29. New viruses in idiopathic human diarrhea cases, the Netherlands

Author

Smits, Saskia L., Schapendonk, Claudia M.E., van Beek, Janko, Vennema, Harry, Schurch, Anita C., Schipper, Debby, Bodewes, Rogier, Haagmans, Bart L., Osterhaus, Albert D.M.E., and Koopmans, Marion P.

Subjects
Gastroenteritis -- Analysis, Diarrhea -- Analysis, Circular DNA -- Analysis, Health
Abstract

The list of emerging viral pathogens is ever-changing. The recognition that an increasing number of diseases that were once unexplained are caused by infectious agents has increased substantially in recent [...]

Published
2014
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30. Underdiagnosis of foodborne hepatitis A, the Netherlands, 2008-2010

Author

Petrignani, Mariska, Verhoef, Linda, Vennema, Harry, van Hunen, Rianne, Baas, Dominique, van Steenbergen, Jim E., and Koopmans, Marion P.G.

Subjects
Hepatitis A -- Health aspects, Infection -- Health aspects, Health
Abstract

Hepatitis A virus (HAV) infection is an acute, usually self-limiting, illness; transmission is associated with suboptimal hygiene. Transmission occurs by the oral route, and infected persons can shed high amounts [...]

Published
2014
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38. An integrated approach to identifying international foodborne norovirus outbreaks

Author

Verhoef, Linda, Kouyos, Roger D., Vennema, Harry, Kroneman, Annelies, Siebenga, Joukje, van Pelt, Wilfrid, and Koopmans, Marion

Subjects
Foodborne diseases -- Distribution -- International aspects -- Genetic aspects, Company distribution practices, Health
Abstract

Noroviruses are the most prevalent causative agents of acute viral gastroenteritis in the community (1-4). Currently, 5 norovirus genogroups have been described and subdivided into at least 40 genotypes (5,6), [...]

Published
2011
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39. Use of norovirus genotype profiles to differentiate origins of foodborne outbreaks

Author

Verhoef, Linda, Vennema, Harry, van Pelt, Wilfrid, Lees, David, Boshuizen, Hendriek, Henshilwood, Kathleen, and Koopmans, Marion

Subjects
Medical research -- Analysis, Medicine, Experimental -- Analysis, Infection -- Genetic aspects -- Analysis, Public health -- Analysis, Disease transmission -- Genetic aspects -- Analysis, Food contamination -- Analysis, Health
Abstract

Noroviruses are members of the family Caliciviridae and recognized as major pathogens in outbreaks of gastroenteritis worldwide. Because these viruses have environmental stability (1), ability to use different transmission routes, [...]

Published
2010
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40. Sources of hepatitis E virus genotype 3 in the Netherlands

Author

Rutjes, Saskia A., Lodder, Willemijn J., Lodder-Verschoor, Froukje, van den Berg, Harold H.J.L., Vennema, Harry, Duizer, Erwin, Koopmans, Marion, and de Roda Husman, Ana Maria

Subjects
Aquatic resources -- Netherlands, Aquatic resources -- Genetic aspects, Aquatic resources -- Health aspects, Disease transmission -- Genetic aspects, Disease transmission -- Health aspects, Farms -- Genetic aspects, Farms -- Health aspects, Hepatitis E -- Genetic aspects, Hepatitis E -- Health aspects, Pork industry -- Genetic aspects, Pork industry -- Health aspects
Abstract

Non-travel-related hepatitis E virus (HEV) genotype 3 infections in persons in the Netherlands may have a zoonotic, foodborne, or water-borne origin. Possible reservoirs for HEV transmission by water, food, and [...]

Published
2009

42. Emergence of new norovirus variants on spring cruise ships and prediction of winter epidemics

Author

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, Gabor, Schreier, Eckart, Siebenga, Joukje, Vainio, Kirsti, Varela, Carmen, Vennema, Harry, and Koopmans, Marion

Subjects
Company distribution practices, Cruise ships -- Environmental aspects, Cruise ships -- Research, Norovirus -- Health aspects, Norovirus -- Genetic aspects, Norovirus -- Distribution, Norovirus -- Research
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 [...]

Published
2008

43. Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands

Author

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

Subjects
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.

Published
2020

44. Rapid SARS-CoV-2 whole genome sequencing for informed public health decision making in the Netherlands

Author

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

Subjects
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.

Published
2020
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46. Usability of the international HAVNet hepatitis A virus database for geographical annotation, backtracing and outbreak detection

Author

Kroneman, Annelies, de Sousa, Rita, Verhoef, Linda, Koopmans, Marion P G, Vennema, Harry, On Behalf Of The HAVNet Network, and Virology

Subjects
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.

Published
2018

47. Early identification of common-source foodborne virus outbreaks in Europe

Author

Koopmans, Marion, Vennema, Harry, Heersma, Herre, van Strien, Elisabeth, van Duynhoven, Yvonne, Myller, Rolf, Reacher, Marc, and Lopman, Ben

Subjects
Technology application, Diseases -- Reporting, Gastroenteritis -- Diagnosis, Foodborne diseases -- Risk factors
Abstract

The importance of foodborne viral infections is increasingly recognized. Food handlers can transmit infection during preparation or serving; fruit and vegetables may be contaminated by fecally contaminated water used for [...]

Published
2003

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