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1. Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans

Author

Munnink, B.B.O. (Bas B. Oude), Sikkema, R.S. (Reina S.), Nieuwenhuijse, D.F. (David F.), Molenaar, R.J. (Robert Jan), Munger, E. (Emmanuelle), Molenkamp, R. (Richard), Van Der Spek, A. (Arco), Tolsma, P. (Paulien), Rietveld, A. (Ariene), Brouwer, M. (Miranda), Bouwmeester-Vincken, N. (Noortje), Harders, F. (Frank), Der Honing, R.H.-V. (Renate Hakze-Van), Wegdam-Blans, M.C. (Marjolijn C.), Bouwstra, R.J. (Ruth J.), Geurts van Kessel, C.H. (Corine), Eijck, A.A. (Annemiek), Velkers, F.C. (Francisca C.), Smit, L.A.M., Stegeman, A. (Arjan), Poel, W.H.M. van der, Koopmans D.V.M., M.P.G. (Marion), Munnink, B.B.O. (Bas B. Oude), Sikkema, R.S. (Reina S.), Nieuwenhuijse, D.F. (David F.), Molenaar, R.J. (Robert Jan), Munger, E. (Emmanuelle), Molenkamp, R. (Richard), Van Der Spek, A. (Arco), Tolsma, P. (Paulien), Rietveld, A. (Ariene), Brouwer, M. (Miranda), Bouwmeester-Vincken, N. (Noortje), Harders, F. (Frank), Der Honing, R.H.-V. (Renate Hakze-Van), Wegdam-Blans, M.C. (Marjolijn C.), Bouwstra, R.J. (Ruth J.), Geurts van Kessel, C.H. (Corine), Eijck, A.A. (Annemiek), Velkers, F.C. (Francisca C.), Smit, L.A.M., Stegeman, A. (Arjan), Poel, W.H.M. van der, and Koopmans D.V.M., M.P.G. (Marion)

Abstract

Animal experiments have shown that nonhuman primates, cats, ferrets, hamsters, rabbits, and bats can be infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In addition, SARS-CoV-2 RNA has been detected in felids, mink, and dogs in the field. Here, we describe an in-depth investigation using whole-genome sequencing of outbreaks on 16 mink farms and the humans living or working on these farms. We conclude that the virus was initially introduced by humans and has since evolved, most likely reflecting widespread circulation among mink in the beginning of the infection period, several weeks before detection. Despite enhanced biosecurity, early warning surveillance, and immediate culling of animals in affected farms, transmission occurred between mink farms in three large transmission clusters with unknown modes of transmission. Of the tested mink farm residents, employees, and/or individuals with whom they had been in contact, 68% had evidence of SARS-CoV-2 infection. Individuals for which whole genomes were available were shown to have been infected with strains with an animal sequence signature, providing evidence of animal-to-human transmission of SARS-CoV-2 within mink farms.

Published
2021
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2. Why psychiatry is different - challenges and difficulties in managing a nosocomial outbreak of coronavirus disease (COVID-19) in hospital care

Author

Rovers, J.J.E. (J. J.E.), van de Linde, L.S. (L. S.), Kenters, N. (N.), Bisseling, E.M. (E. M.), Nieuwenhuijse, D.F. (David F.), Oude Munnink, B.B. (Bas B.), Voss, A. (A.), Nabuurs-Franssen, M. (M.), Rovers, J.J.E. (J. J.E.), van de Linde, L.S. (L. S.), Kenters, N. (N.), Bisseling, E.M. (E. M.), Nieuwenhuijse, D.F. (David F.), Oude Munnink, B.B. (Bas B.), Voss, A. (A.), and Nabuurs-Franssen, M. (M.)

Abstract

Objective: Coronavirus disease (COVID-19) was officially declared a pandemic in March 2020. Many cases of COVID-19 are nosocomial, but to the best of our knowledge, no nosocomial outbreaks on psychiatric departments of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported in Europe. The different nature of psychiatry makes outbreak management more difficult. This study determines which psychiatry specific factors contributed to a nosocomial outbreak taking place in a psychiatric department. This will provide possible interventions in future outbreak management. Method: A case series describing a nosocomial outbreak in a psychiatric department of an acute care hospital in the Netherlands between March 13, 2020 and April, 14 2020. The outbreak was analyzed by combining data from standardized interviews, polymerase chain reaction (PCR) tests and whole genome sequencing (WGS). Results: The nosocomial outbreak in which 43% of staff of the psychiatric department and 19% of admitted patients were involved, was caused by healthcare worker (HCW)-to-HCW transmissions, as well as patient-to-HCW-to-patient transmission. We identified four aspects associated with the mental health care system which might have made our department more susceptible to an outbreak. Conclusions: Infection control measures designed for hospitals are not directly applicable to psychiatric departments. Psychiatric patients should be considered a high-risk group for infectious diseases and customized measures should be designed and implemented. Extra attention for psychiatric departments is necessary during a pandemic as psychiatric HCWs are less familiar with outbreak management. Clear communication and governance is crucial in correctly implementing these measures.

Published
2020
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3. The International Virus Bioinformatics Meeting 2020

Author

Hufsky, F. (Franziska), Beerenwinkel, N. (Niko), Meyer, I.M. (Irmtraud M.), Roux, S. (Simon), Cook, G.M. (Georgia May), Kinsella, C.M. (Cormac M.), Lamkiewicz, K. (Kevin), Marquet, M. (Mike), Nieuwenhuijse, D.F. (David F.), Olendraite, I. (Ingrida), Paraskevopoulou, S. (Sofia), Young, F. (Francesca), Dijkman, R. (Ronald), Ibrahim, B. (Bashar), Kelly, J. (Jenna), Le Mercier, P. (Philippe), Marz, M. (Manja), Ramette, A. (Alban), Thiel, V. (Volker), Hufsky, F. (Franziska), Beerenwinkel, N. (Niko), Meyer, I.M. (Irmtraud M.), Roux, S. (Simon), Cook, G.M. (Georgia May), Kinsella, C.M. (Cormac M.), Lamkiewicz, K. (Kevin), Marquet, M. (Mike), Nieuwenhuijse, D.F. (David F.), Olendraite, I. (Ingrida), Paraskevopoulou, S. (Sofia), Young, F. (Francesca), Dijkman, R. (Ronald), Ibrahim, B. (Bashar), Kelly, J. (Jenna), Le Mercier, P. (Philippe), Marz, M. (Manja), Ramette, A. (Alban), and Thiel, V. (Volker)

Abstract

The International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8-9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online. On the other hand, the pandemic has made us even more aware of the importance of accelerating research in viral bioinformatics. Advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks. The International Virus Bioinformatics Meeting 2020 has attracted approximately 120 experts in virology and bioinformatics from all over the world to join the two-day virtual meeting. Despite concerns being raised that virtual meetings lack possibilities for face-to-face discussion, the participants from this small community created a highly interactive scientific environment, engaging in lively and inspiring discussions and suggesting new research directions and questions. The meeting featured five invited and twelve contributed talks, on the four main topics: (1) proteome and RNAome of R

Published
2020
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4. Setting a baseline for global urban virome surveillance in sewage

Author

Nieuwenhuijse, D.F. (David F.), Oude Munnink, B.B. (Bas B.), Phan, M.V.T. (My V. T.), Hendriksen, R.S. (Rene S.), Bego, A. (Artan), Rees, C. (Catherine), Neilson, E.H. (Elizabeth Heather), Coventry, K. (Kris), Collignon, P. (Peter), Allerberger, F. (Franz), Rahube, T.O. (Teddie O.), Oliveira, G. (Guilherme), Ivanov, I. (Ivan), Sopheak, T. (Thet), Vuthy, Y. (Yith), Yost, C.K. (Christopher K.), Tabo, D.-A. (Djim-adjim), Cuadros-Orellana, S. (Sara), Ke, C. (Changwen), Zheng, H. (Huanying), Baisheng, L. (Li), Jiao, X. (Xiaoyang), Donado-Godoy, P. (Pilar), Coulibaly, K.J. (Kalpy Julien), Hrenovic, J. (Jasna), Jergović, M. (Matijana), Karpíšková, R. (Renáta), Elsborg, B. (Bodil), Legesse, M. (Mengistu), Eguale, T. (Tadesse), Heikinheimo, A. (Annamari), Villacis, J.E. (Jose Eduardo), Sanneh, B. (Bakary), Malania, L. (Lile), Nitsche, A., Brinkmann, A. (Annika), Saba, C.K.S. (Courage Kosi Setsoafia), Kocsis, B. (Bela), Solymosi, N. (Norbert), Thorsteinsdottir, T.R. (Thorunn R.), Hatha, A.M. (Abdulla Mohamed), Alebouyeh, M. (Masoud), Morris, D. (Douglas), O’Connor, L. (Louise), Cormican, M. (M.), Moran-Gilad, J. (Jacob), Battisti, A. (Antonio), Alba, P. (Patricia), Shakenova, Z. (Zeinegul), Kiiyukia, C. (Ciira), Ng’eno, E. (Eric), Raka, L. (Lul), Bērziņš, A. (Aivars), Avsejenko, J. (Jeļena), Bartkevics, V. (Vadims), Penny, C. (Christian), Rajandas, H. (Heraa), Parimannan, S. (Sivachandran), Haber, M.V. (Malcolm Vella), Pal, P. (Pushkar), Schmitt, H. (Heike), van Passel, M. (Mark), van de Schans, M.G.M. (Milou G.M.), Zuidema, T. (Tina), Jeunen, G.-J. (Gert-Jan), Gemmell, N. (Neil), Fashae, K. (Kayode), Wester, A.L. (Astrid Louise), Holmstad, R. (Rune), Hasan, R. (Rumina), Shakoor, S. (Sadia), Rojas, M.L.Z. (Maria Luz Zamudio), Wasyl, D. (Dariusz), Bosevska, G. (Golubinka), Kochubovski, M. (Mihail), Radu, C. (Cojocaru), Gassama†, A. (Amy), Radosavljevic, V. (Vladimir), Tay, M.Y.F. (Moon Y.F.), Zuniga-Montanez, R. (Rogelio), Wuertz, S. (Stefan), Gavačová, D. (Dagmar), Trkov, M. (Marija), Keddy, K. (Karen), Esterhuyse, K. (Kerneels), Cerdà-Cuéllar, M. (Marta), Pathirage, S. (Sujatha), Larsson, D.G.J. (D.G.Joakim), Norrgren, L. (Leif), Örn, S. (Stefan), Van der Heijden, T. (Tanja), Kumburu, H.H. (Happiness Houka), de RodaHusman, A.M. (Ana Maria), Njanpop-Lafourcade, B.-M. (Berthe-Marie), Bidjada, P. (Pawou), Nikiema-Pessinaba, S.C. (Somtinda Christelle), Levent, B. (Belkis), Meschke, J.S. (John Scott), Beck, N.K. (Nicola Koren), Van Dang, C. (Chinh), Tran, D.M.N. (Doan Minh Nguyen), Do Phuc, N. (Nguyen), Kwenda, G. (Geoffrey), Munk, P. (Patrick), Venkatakrishnan, S. (Shweta), Aarestrup, F.M. (Frank), Cotten, M. (Matthew), Koopmans D.V.M., M.P.G. (Marion), Nieuwenhuijse, D.F. (David F.), Oude Munnink, B.B. (Bas B.), Phan, M.V.T. (My V. T.), Hendriksen, R.S. (Rene S.), Bego, A. (Artan), Rees, C. (Catherine), Neilson, E.H. (Elizabeth Heather), Coventry, K. (Kris), Collignon, P. (Peter), Allerberger, F. (Franz), Rahube, T.O. (Teddie O.), Oliveira, G. (Guilherme), Ivanov, I. (Ivan), Sopheak, T. (Thet), Vuthy, Y. (Yith), Yost, C.K. (Christopher K.), Tabo, D.-A. (Djim-adjim), Cuadros-Orellana, S. (Sara), Ke, C. (Changwen), Zheng, H. (Huanying), Baisheng, L. (Li), Jiao, X. (Xiaoyang), Donado-Godoy, P. (Pilar), Coulibaly, K.J. (Kalpy Julien), Hrenovic, J. (Jasna), Jergović, M. (Matijana), Karpíšková, R. (Renáta), Elsborg, B. (Bodil), Legesse, M. (Mengistu), Eguale, T. (Tadesse), Heikinheimo, A. (Annamari), Villacis, J.E. (Jose Eduardo), Sanneh, B. (Bakary), Malania, L. (Lile), Nitsche, A., Brinkmann, A. (Annika), Saba, C.K.S. (Courage Kosi Setsoafia), Kocsis, B. (Bela), Solymosi, N. (Norbert), Thorsteinsdottir, T.R. (Thorunn R.), Hatha, A.M. (Abdulla Mohamed), Alebouyeh, M. (Masoud), Morris, D. (Douglas), O’Connor, L. (Louise), Cormican, M. (M.), Moran-Gilad, J. (Jacob), Battisti, A. (Antonio), Alba, P. (Patricia), Shakenova, Z. (Zeinegul), Kiiyukia, C. (Ciira), Ng’eno, E. (Eric), Raka, L. (Lul), Bērziņš, A. (Aivars), Avsejenko, J. (Jeļena), Bartkevics, V. (Vadims), Penny, C. (Christian), Rajandas, H. (Heraa), Parimannan, S. (Sivachandran), Haber, M.V. (Malcolm Vella), Pal, P. (Pushkar), Schmitt, H. (Heike), van Passel, M. (Mark), van de Schans, M.G.M. (Milou G.M.), Zuidema, T. (Tina), Jeunen, G.-J. (Gert-Jan), Gemmell, N. (Neil), Fashae, K. (Kayode), Wester, A.L. (Astrid Louise), Holmstad, R. (Rune), Hasan, R. (Rumina), Shakoor, S. (Sadia), Rojas, M.L.Z. (Maria Luz Zamudio), Wasyl, D. (Dariusz), Bosevska, G. (Golubinka), Kochubovski, M. (Mihail), Radu, C. (Cojocaru), Gassama†, A. (Amy), Radosavljevic, V. (Vladimir), Tay, M.Y.F. (Moon Y.F.), Zuniga-Montanez, R. (Rogelio), Wuertz, S. (Stefan), Gavačová, D. (Dagmar), Trkov, M. (Marija), Keddy, K. (Karen), Esterhuyse, K. (Kerneels), Cerdà-Cuéllar, M. (Marta), Pathirage, S. (Sujatha), Larsson, D.G.J. (D.G.Joakim), Norrgren, L. (Leif), Örn, S. (Stefan), Van der Heijden, T. (Tanja), Kumburu, H.H. (Happiness Houka), de RodaHusman, A.M. (Ana Maria), Njanpop-Lafourcade, B.-M. (Berthe-Marie), Bidjada, P. (Pawou), Nikiema-Pessinaba, S.C. (Somtinda Christelle), Levent, B. (Belkis), Meschke, J.S. (John Scott), Beck, N.K. (Nicola Koren), Van Dang, C. (Chinh), Tran, D.M.N. (Doan Minh Nguyen), Do Phuc, N. (Nguyen), Kwenda, G. (Geoffrey), Munk, P. (Patrick), Venkatakrishnan, S. (Shweta), Aarestrup, F.M. (Frank), Cotten, M. (Matthew), and Koopmans D.V.M., M.P.G. (Marion)

Abstract

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective.

Published
2020
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5. COVID-19 in health-care workers in three hospitals in the south of the Netherlands: a cross-sectional study

Author

Sikkema, R.S. (Reina S), Pas, S.D. (Suzan), Nieuwenhuijse, D.F. (David F.), O'Toole, Á. (Áine), Verweij, J. (Jaco), Linden, A. van der, Chestakova, I. (Irina), Schapendonk, C.M.E. (Claudia), Pronk, M.R. (Mark), Lexmond, P. (Pascal), Bestebroer, T.M. (Theo), Overmars, R.J. (Ronald J), Nieuwkoop, S. (Stefan) van, van den Bijllaardt, W. (Wouter), Bentvelsen, R.G. (Robbert G), Rijen, M.M.L. (Miranda) van, Buiting, A.G.M. (Anton), van Oudheusden, A.J.G. (Anne J G), Diederen, B.M.W. (Bram), Bergmans, D.C. (Tom), Eijck, A.A. (Annemiek), Molenkamp, R. (Richard), Rambaut, A. (Andrew), Timen, A. (Aura), Kluytmans, J.A.J.W. (Jan), Oude Munnink, B.B. (Bas B.), Kluytmans-Vandenbergh, M.F.Q. (Marjolein), Koopmans D.V.M., M.P.G. (Marion), Sikkema, R.S. (Reina S), Pas, S.D. (Suzan), Nieuwenhuijse, D.F. (David F.), O'Toole, Á. (Áine), Verweij, J. (Jaco), Linden, A. van der, Chestakova, I. (Irina), Schapendonk, C.M.E. (Claudia), Pronk, M.R. (Mark), Lexmond, P. (Pascal), Bestebroer, T.M. (Theo), Overmars, R.J. (Ronald J), Nieuwkoop, S. (Stefan) van, van den Bijllaardt, W. (Wouter), Bentvelsen, R.G. (Robbert G), Rijen, M.M.L. (Miranda) van, Buiting, A.G.M. (Anton), van Oudheusden, A.J.G. (Anne J G), Diederen, B.M.W. (Bram), Bergmans, D.C. (Tom), Eijck, A.A. (Annemiek), Molenkamp, R. (Richard), Rambaut, A. (Andrew), Timen, A. (Aura), Kluytmans, J.A.J.W. (Jan), Oude Munnink, B.B. (Bas B.), Kluytmans-Vandenbergh, M.F.Q. (Marjolein), and Koopmans D.V.M., M.P.G. (Marion)

Abstract

Background: 10 days after the first reported case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the Netherlands (on Feb 27, 2020), 55 (4%) of 1497 health-care workers in nine hospitals located in the south of the Netherlands had tested positive for SARS-CoV-2 RNA. We aimed to gain insight in possible sources of infection in health-care workers. Methods: We did a cross-sectional study at three of the nine hospitals located in the south of the Netherlands. We screened health-care workers at the participating hospitals for SARS-CoV-2 infection, based on clinical symptoms (fever or mild respiratory symptoms) in the 10 days before screening. We obtained epidemiological data through structured interviews with health-care workers and combined this information with data from whole-genome sequencing of SARS-CoV-2 in clinical samples taken from health-care workers and patients. We did an in-depth analysis of sources and modes of transmission of SARS-CoV-2 in health-care workers and patients. Findings: Between March 2 and March 12, 2020, 1796 (15%) of 12 022 health-care workers were screened, of whom 96 (5%) tested positive for SARS-CoV-2. We obtained complete and near-complete genome sequences from 50 health-care workers and ten patients. Most sequences were grouped in three clusters, with two clusters showing local circulation within the region. The noted patterns were consistent with multiple introductions into the hospitals through community-acquired infections and local amplification in the community. Interpretation: Although direct transmission in the hospitals cannot be ruled out, our data do not support widespread nosocomial transmission as the source of infection in patients or health-care workers. Funding: EU Horizon 2020 (RECoVer, VEO, and the European Joint Programme One Health METASTAVA), and the National Institute of Allergy and Infectious Diseases, National Institutes of Health.

Published
2020
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6. Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Author

Oude Munnink, B.B. (Bas B.), Nieuwenhuijse, D.F. (David F.), Sikkema, R.S. (Reina S.), Koopmans D.V.M., M.P.G. (Marion), Oude Munnink, B.B. (Bas B.), Nieuwenhuijse, D.F. (David F.), Sikkema, R.S. (Reina S.), and Koopmans D.V.M., M.P.G. (Marion)

Abstract

Whole genome sequencing can be used to characterize and to trace viral outbreaks. Nanopore-based whole genome sequencing protocols have been described for several different viruses. These approaches utilize an overlapping amplicon-based approach which can be used to target a specific virus or group of genetically related viruses. In addition to confirmation of the virus presence, sequencing can be used for genomic epidemiology studies, to track viruses and unravel origins, reservoirs and modes of transmission. For such applications, it is crucial to understand possible effects of the error rate associated with the platform used. Routine application in clinical and public health settings require that this is documented with every important change in the protocol. Previously, a protocol for whole genome Usutu virus sequencing on the nanopore sequencing platform was validated (R9.4 flowcell) by direct comparison to Illumina sequencing. Here, we describe the method used to determine the required read coverage, using the comparison between the R10

Published
2020
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7. Genomic monitoring to understand the emergence and spread of Usutu virus in the Netherlands, 2016-2018

Author

Oude Munnink, B.B. (Bas B.), Münger, E. (E.), Nieuwenhuijse, D.F. (David F.), Kohl, R.H.G., Linden, A. van der, Schapendonk, C.M.E. (Claudia), van der Jeugd, H.P., Kik, M.J.L. (Marja), Rijks, J.M. (Jolianne), Reusken, C.B.E.M. (Chantal), Koopmans, M. (M.), Oude Munnink, B.B. (Bas B.), Münger, E. (E.), Nieuwenhuijse, D.F. (David F.), Kohl, R.H.G., Linden, A. van der, Schapendonk, C.M.E. (Claudia), van der Jeugd, H.P., Kik, M.J.L. (Marja), Rijks, J.M. (Jolianne), Reusken, C.B.E.M. (Chantal), and Koopmans, M. (M.)

Abstract

Usutu virus (USUV) is a mosquito-borne flavivirus circulating in Western Europe that causes die-offs of mainly common blackbirds (Turdus merula). In the Netherlands, USUV was first detected in 2016, when it was identified as the likely cause of an outbreak in birds. In this study, dead blackbirds were collected, screened for the presence of USUV and submitted to Nanopore-based sequencing. Genomic sequences

Published
2020
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8. Virus Metagenomics in Farm Animals: A Systematic Review

Author

Kwok, K.T.T. (Kirsty T T), Nieuwenhuijse, D.F. (David F.), Phan, M.V.T. (My V T), Koopmans, M.P.G. (Marion P G), Kwok, K.T.T. (Kirsty T T), Nieuwenhuijse, D.F. (David F.), Phan, M.V.T. (My V T), and Koopmans, M.P.G. (Marion P G)

Abstract

A majority of emerging infectious diseases are of zoonotic origin. Metagenomic Next-Generation Sequencing (mNGS) has been employed to identify uncommon and novel infectious etiologies and characterize virus diversity in human, animal, and environmental samples. Here, we systematically reviewed studies that performed viral mNGS in common livestock (cattle, small ruminants, poultry, and pigs). We identified 2481 records and 120 records were ultimately included after a first and second screening. Pigs were the most frequently studied livestock and the virus diversity found in samples from poultry was the highest. Known animal viruses, zoonotic viruses, and novel viruses were reported in available literature, demonstrating the capacity of mNGS to identify both known and novel viruses. However, the coverage of metagenomic studies was patchy, with few data on the virome of small ruminants and respiratory virome of studied livestock. Essential metadata such as age of livestock and farm types were rarely mentioned in available literature, and only 10.8% of the datasets were publicly available. Developing a deeper understanding of livestock virome is crucial for detection of potential zoonotic and animal pathogens and One Health preparedness. Metagenomic studies can provide this background but only when combined with essential metadata and following the "FAIR" (Findable, Accessible, Interoperable, and Reusable) data principles.

Published
2020
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9. The COMPARE Data Hubs

Author

Amid, C. (Clara), Pakseresht, N. (Nima), Silvester, N. (Nicole), Jayathilaka, S. (Suran), Lund, O. (Ole), Dynovski, L.D. (Lukasz D.), Pataki, B.Á. (Bálint Á), Visontai, D. (Dávid), Xavier, B.B. (Basil Britto), Alako, B.T.F. (Blaise), Belka, A. (Ariane), Cisneros, J.L.B. (Jose L B), Cotten, M. (Matthew), Haringhuizen, G.B. (George B.), Harrison, P.W. (Peter W.), Höper, D. (Dirk), Holt, S. (Sam), Hundahl, C. (Camilla), Hussein, A. (Abdulrahman), Kaas, R.S. (Rolf S.), Liu, X. (Xin), Leinonen, R. (Rasko), Malhotra-Kumar, S. (Surbhi), Nieuwenhuijse, D.F. (David F.), Rahman, N. (Nadim), Dos S Ribeiro, C. (Carolina), Skiby, J.E. (Jeffrey E.), Schmitz, D. (Dennis), Stéger, J. (József), Szalai-Gindl, J.M. (János M), Thomsen, M.C.F. (Martin C F), Caccio, S. (Simone), Csabai, I. (István), Kroneman, A. (Annelies), Koopmans D.V.M., M.P.G. (Marion), Aarestrup, F.M. (Frank), Cochrane, G. (Guy), Amid, C. (Clara), Pakseresht, N. (Nima), Silvester, N. (Nicole), Jayathilaka, S. (Suran), Lund, O. (Ole), Dynovski, L.D. (Lukasz D.), Pataki, B.Á. (Bálint Á), Visontai, D. (Dávid), Xavier, B.B. (Basil Britto), Alako, B.T.F. (Blaise), Belka, A. (Ariane), Cisneros, J.L.B. (Jose L B), Cotten, M. (Matthew), Haringhuizen, G.B. (George B.), Harrison, P.W. (Peter W.), Höper, D. (Dirk), Holt, S. (Sam), Hundahl, C. (Camilla), Hussein, A. (Abdulrahman), Kaas, R.S. (Rolf S.), Liu, X. (Xin), Leinonen, R. (Rasko), Malhotra-Kumar, S. (Surbhi), Nieuwenhuijse, D.F. (David F.), Rahman, N. (Nadim), Dos S Ribeiro, C. (Carolina), Skiby, J.E. (Jeffrey E.), Schmitz, D. (Dennis), Stéger, J. (József), Szalai-Gindl, J.M. (János M), Thomsen, M.C.F. (Martin C F), Caccio, S. (Simone), Csabai, I. (István), Kroneman, A. (Annelies), Koopmans D.V.M., M.P.G. (Marion), Aarestrup, F.M. (Frank), and Cochrane, G. (Guy)

Abstract

Data sharing enables research communities to exchange findings and build upon the knowledge that arises from their discoveries. Areas of public and animal health as well as food safety would benefit from rapid data sharing when it comes to emergencies. However, ethical, regulatory and institutional challenges, as well as lack of suitable platforms which provide an infrastructure for data sharing in structured formats, often lead to data not being shared or at most shared in form of supplementary materials in journal publications. Here, we describe an informatics platform that includes workflows for structured data storage, managing and pre-publication sharing of pathogen sequencing data and its analysis interpretations with relevant stakeholders.

Published
2019
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10. Metavirome sequencing to evaluate norovirus diversity in sewage and related bioaccumulated oysters

Author

Strubbia, S. (Sofia), Schaeffer, J. (Julien), Oude Munnink, B.B. (Bas B.), Besnard, A. (Alban), Phan, M.V.T. (My V. T.), Nieuwenhuijse, D.F. (David F.), Graaf, M. (Miranda) de, Schapendonk, C.M.E. (Claudia), Wacrenier, C. (Candice), Cotten, M. (Matthew), Koopmans D.V.M., M.P.G. (Marion), Le Guyader, F.S. (Françoise S.), Strubbia, S. (Sofia), Schaeffer, J. (Julien), Oude Munnink, B.B. (Bas B.), Besnard, A. (Alban), Phan, M.V.T. (My V. T.), Nieuwenhuijse, D.F. (David F.), Graaf, M. (Miranda) de, Schapendonk, C.M.E. (Claudia), Wacrenier, C. (Candice), Cotten, M. (Matthew), Koopmans D.V.M., M.P.G. (Marion), and Le Guyader, F.S. (Françoise S.)

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

Published
2019
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11. Studies into the mechanism of measles-associated immune suppression during a measles outbreak in the Netherlands

Author

Laksono, B.M. (Brigitta), Vries, R.D. (Rory) de, Verburgh, R.J. (Joyce), Visser, E. (Eline), de Jong, A. (Alwin), Fraaij, P.L.A. (Pieter), Ruijs, W.L.M. (Wilhelmina L.M.), Nieuwenhuijse, D.F. (David F.), Ham, H.J. van den, Koopmans D.V.M., M.P.G. (Marion), Zelm, M.C. (Menno) van, Osterhaus, A.D.M.E. (Albert D M E), Swart, R.L. (Rik) de, Laksono, B.M. (Brigitta), Vries, R.D. (Rory) de, Verburgh, R.J. (Joyce), Visser, E. (Eline), de Jong, A. (Alwin), Fraaij, P.L.A. (Pieter), Ruijs, W.L.M. (Wilhelmina L.M.), Nieuwenhuijse, D.F. (David F.), Ham, H.J. van den, Koopmans D.V.M., M.P.G. (Marion), Zelm, M.C. (Menno) van, Osterhaus, A.D.M.E. (Albert D M E), and Swart, R.L. (Rik) de

Abstract

Measles causes a transient immune suppression, leading to increased susceptibility to opportunistic infections. In experimentally infected non-human primates (NHPs) measles virus (MV) infects and depletes pre-existing memory lymphocytes, causing immune amnesia. A measles outbreak in the Dutch Orthodox Protes

Published
2018
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12. Metagenomic sequencing for surveillance of food- and waterborne viral diseases

Author

Nieuwenhuijse, D.F. (David F.), Koopmans D.V.M., M.P.G. (Marion), Nieuwenhuijse, D.F. (David F.), and Koopmans D.V.M., M.P.G. (Marion)

Abstract

A plethora of viruses can be transmitted by the food- and waterborne route. However, their recognition is challenging because of the variety of viruses, heterogeneity of symptoms, the lack of awareness of clinicians, and limited surveillance efforts. Classical food- and waterborne viral disease outbreaks are mainly caused by caliciviruses, but the source of the virus is often not known and the foodborne mode of transmission is difficult to discriminate from human-to-human transmission. Atypical food- and waterborne viral disease can be caused by viruses such as hepatitis A and hepatitis E. In addition, a source of novel emerging viruses with a potential to spread via the food- and waterborne route is the repeated interaction of humans with wildlife. Wildlife-to-human adaptation may give rise to self- limiting outbreaks in some cases, but when fully adjusted to the human host can be devastating. Metagenomic sequencing has been investigated as a promising solution for surveillance purposes as it detects all viruses in a single protocol, delivers additional genomic information for outbreak tracing, and detects novel unknown viruses. Nevertheless, several issues must be addressed to apply metagenomic sequencing in surveillance. First, sample preparation is difficult since the genomic material of viruses is general

Published
2017
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