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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. Duration and key determinants of infectious virus shedding in hospitalized patients with coronavirus disease-2019 (COVID-19)

Author

Kampen, J.J.A. (Jeroen) van, Vijver, D.A.M.C. (David) van de, Fraaij, P.L.A. (Pieter), Haagmans, B.L. (Bart), Lamers, M.M. (Mart M.), Okba, N.M.A. (Nisreen), Van Den Akker, J.P.C., Endeman, H. (Henrik), Gommers, D.A.M.P.J. (Diederik), Cornelissen, J.J. (Jan), Hoek, R.A.S. (Rogier), Eerden, M. (Menno) van der, Hesselink, D.A. (Dennis), Metselaar, H.J. (Herold), Verbon, A. (Annelies), Steenwinkel, J.E.M. (Jurriaan) de, Aron, G.I. (Georgina), Gorp, E.C.M. (Eric) van, Boheemen, S. (Sander) van, Voermans, J. (Jolanda), Boucher, C.A.B. (Charles), Molenkamp, R. (Richard), Koopmans D.V.M., M.P.G. (Marion), Geurts van Kessel, C.H. (Corine), Eijck, A.A. (Annemiek), Kampen, J.J.A. (Jeroen) van, Vijver, D.A.M.C. (David) van de, Fraaij, P.L.A. (Pieter), Haagmans, B.L. (Bart), Lamers, M.M. (Mart M.), Okba, N.M.A. (Nisreen), Van Den Akker, J.P.C., Endeman, H. (Henrik), Gommers, D.A.M.P.J. (Diederik), Cornelissen, J.J. (Jan), Hoek, R.A.S. (Rogier), Eerden, M. (Menno) van der, Hesselink, D.A. (Dennis), Metselaar, H.J. (Herold), Verbon, A. (Annelies), Steenwinkel, J.E.M. (Jurriaan) de, Aron, G.I. (Georgina), Gorp, E.C.M. (Eric) van, Boheemen, S. (Sander) van, Voermans, J. (Jolanda), Boucher, C.A.B. (Charles), Molenkamp, R. (Richard), Koopmans D.V.M., M.P.G. (Marion), Geurts van Kessel, C.H. (Corine), and Eijck, A.A. (Annemiek)

Abstract

Key questions in COVID-19 are the duration and determinants of infectious virus shedding. Here, we report that infectious virus shedding is detected by virus cultures in 23 of the 129 patients (17.8%) hospitalized with COVID-19. The median duration of shedding infectious virus is 8 days post onset of symptoms (IQR 5–11) and drops below 5% after 15.2 days post onset of symptoms (95% confidence interval (CI) 13.4–17.2). Multivariate analyses identify viral loads above 7 log10 RNA copies/mL (odds ratio [OR] of 14.7 (CI 3.57-58.1; p < 0.001) as independently associated with isolation of infectious SARS-CoV-2 from the respiratory tract. A serum neutralizing antibody titre of at least 1:20 (OR of 0.01 (CI 0.003-0.08; p < 0.001) is independently associated with non-infectious SARS-CoV-2. We conclude that quantitative viral RNA load assays and serological assays could be used in test-based strategies to discontinue or de-escalate infection prevention and control precautions.

Published
2021
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3. An organoid-derived bronchioalveolar model for SARS-CoV-2 infection of human alveolar type II-like cells

Author

Lamers, M.M. (Mart M.), van der Vaart, J. (Jelte), Knoops, K. (Kèvin), Riesebosch, S. (Samra), Breugem, T.I. (Tim I), Mykytyn, A.Z. (Anna Z), Beumer, J. (Joep), Schipper, D. (Debby), Bezstarosti, K. (Karel), Koopman, C.D. (Charlotte D), Groen, N. (Nathalie), Ravelli, R.B.G. (Raimond B.), Duimel, H.Q. (Hans Q), Demmers, J.A.A. (Jeroen), Verjans, G.M.G.M. (George), Koopmans D.V.M., M.P.G. (Marion), Muraro, M.J. (Mauro J), Peters, P.J. (Peter J), Clevers, H.C. (Hans), Haagmans, B.L. (Bart), Lamers, M.M. (Mart M.), van der Vaart, J. (Jelte), Knoops, K. (Kèvin), Riesebosch, S. (Samra), Breugem, T.I. (Tim I), Mykytyn, A.Z. (Anna Z), Beumer, J. (Joep), Schipper, D. (Debby), Bezstarosti, K. (Karel), Koopman, C.D. (Charlotte D), Groen, N. (Nathalie), Ravelli, R.B.G. (Raimond B.), Duimel, H.Q. (Hans Q), Demmers, J.A.A. (Jeroen), Verjans, G.M.G.M. (George), Koopmans D.V.M., M.P.G. (Marion), Muraro, M.J. (Mauro J), Peters, P.J. (Peter J), Clevers, H.C. (Hans), and Haagmans, B.L. (Bart)

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), which may result in acute respiratory distress syndrome (ARDS), multiorga

Published
2021
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4. Hand hygiene and glove use in nursing homes before and after an intervention

Author

Teesing, G.R. (Gwen R.), Richardus, J.H. (Jan Hendrik), Erasmus, V. (Vicky), Petrignani, M. (Mariska), Koopmans D.V.M., M.P.G. (Marion), Vos, M.C. (Margreet C.), Schols, J.M.G.A. (Jos), Voeten, H.A.C.M. (Hélène), Teesing, G.R. (Gwen R.), Richardus, J.H. (Jan Hendrik), Erasmus, V. (Vicky), Petrignani, M. (Mariska), Koopmans D.V.M., M.P.G. (Marion), Vos, M.C. (Margreet C.), Schols, J.M.G.A. (Jos), and Voeten, H.A.C.M. (Hélène)

Abstract

We investigated whether an intervention to improve hand hygiene compliance in nursing homes changed glove use. Hand hygiene compliance increased, but substitution of hand hygiene with gloves did not decrease. We observed a reduction of inappropriately unchanged gloves after exposure to body fluids. Clinical trials identifier: Netherlands Trial Register, trial NL6049 (NTR6188): Https://www.trialregister.nl/trial/6049.

Published
2020
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5. Phylogenetic Investigation of Norovirus Transmission between Humans and Animals

Author

Villabruna, N., Izquierdo Lara, R.W., Szarvas, J., Koopmans D.V.M., M.P.G. (Marion), van der Graaf, M., Villabruna, N., Izquierdo Lara, R.W., Szarvas, J., Koopmans D.V.M., M.P.G. (Marion), and van der Graaf, M.

Abstract

Norovirus infections are a leading cause of acute gastroenteritis worldwide, affecting people of all ages. There are 10 norovirus genogroups (GI-GX) that infect humans and animals in a host-specific manner. New variants and genotypes frequently emerge, and their origin is not well understood. One hypothesis is that new human infections may be seeded from an animal reservoir, as human noroviruses have occasionally been detected in animal species. The majority of these sequences were identified as older GII.4 variants, but a variety of other GIIs and GIs have been detected as well. While these sequences share at least 94% nt similarity with human strains, most of them are >98% identical to human strains. The fact that these strains were detected in a

Published
2020
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6. Transmission of NS5A-Inhibitor Resistance-Associated Substitutions among Men Who Have Sex with Men Recently Infected with Hepatitis C Virus Genotype 1a

Author

Popping, S. (Stephanie), Verwijs, R., Cuypers, L., Claassen, M.A.A. (Mark), van den Berk, G.E., De Weggheleire, A., Arends, J.E.A., Boerekamps, A. (Anne), Molenkamp, R., Koopmans D.V.M., M.P.G. (Marion), Verbon, A. (Annelies), Boucher, C.A.B. (Charles), Rijnders, B.J.A. (Bart), Vijver, D.A.M.C. (David) van de, Lauw, F., Posthouwer, D. (Dirk), Hullegie, S., Bierman, W., Dofferhof, A., Kootstra, G.J., Leyten, E, Hollander, J.C. (Jan) den, van Kasteren, M, Soutekouw, R., Ammerlaan, H, Florence, E., Popping, S. (Stephanie), Verwijs, R., Cuypers, L., Claassen, M.A.A. (Mark), van den Berk, G.E., De Weggheleire, A., Arends, J.E.A., Boerekamps, A. (Anne), Molenkamp, R., Koopmans D.V.M., M.P.G. (Marion), Verbon, A. (Annelies), Boucher, C.A.B. (Charles), Rijnders, B.J.A. (Bart), Vijver, D.A.M.C. (David) van de, Lauw, F., Posthouwer, D. (Dirk), Hullegie, S., Bierman, W., Dofferhof, A., Kootstra, G.J., Leyten, E, Hollander, J.C. (Jan) den, van Kasteren, M, Soutekouw, R., Ammerlaan, H, and Florence, E.

Published
2020
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7. SARS-CoV-2-Specific Antibody Detection for Seroepidemiology: A Multiplex Analysis Approach Accounting for Accurate Seroprevalence

Author

den Hartog, G., Schepp, R.M., Kuijer, M., GeurtsvanKessel, C., Beek, J.H.G.M. (Janko) van, Rots, N., Koopmans D.V.M., M.P.G. (Marion), van der Klis, FRM, van Binnendijk, RS, den Hartog, G., Schepp, R.M., Kuijer, M., GeurtsvanKessel, C., Beek, J.H.G.M. (Janko) van, Rots, N., Koopmans D.V.M., M.P.G. (Marion), van der Klis, FRM, and van Binnendijk, RS

Abstract

Background. The COVID-19 pandemic necessitates better understanding of the kinetics of antibody production induced by infection with SARS-CoV-2. We aimed to develop a high-throughput multiplex assay to detect antibodies to SARS-CoV-2 to assess immunity to the virus in the general population. Methods. Spike protein subunits S1 and receptor binding domain, and nucleoprotein were coupled to microspheres. Sera collected before emergence of SARS-CoV-2 (n = 224) and of non-SARS-CoV-2 influenza-like illness (n = 184), and laboratory-confirmed cases of SARS-CoV-2 infection (n = 115) with various severities of COVID-19 were tested for SARS-CoV-2–specific IgG concentrations. Results. Our assay discriminated SARS-CoV-2–induced antibodies and those induced by other viruses. The assay specificity was 95.1%–99.0% with sensitivity 83.6%–95.7%. By merging the test results for all 3 antigens a specificity of 100% was achieved with a sensitivity of at least 90%. Hospitalized COVID-19 patients developed higher IgG concentrations and the rate of IgG production i

Published
2020
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8. Genome sequences of seven megrivirus strains from chickens in the Netherlands

Author

Kwok, K.T.T., de Rooij, M.M.T., Messink, A.B., Wouters, I.M., Koopmans D.V.M., M.P.G. (Marion), Phan, M.V.T., Kwok, K.T.T., de Rooij, M.M.T., Messink, A.B., Wouters, I.M., Koopmans D.V.M., M.P.G. (Marion), and Phan, M.V.T.

Abstract

We report seven chicken megrivirus genome sequences identified in chicken fecal samples from a broiler farm in The Netherlands. The sequences were determined using metagenomic sequencing and would expand our understanding of the genome diversity of megriviruses.

Published
2020
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9. Exploring utility of genomic epidemiology to trace origins of highly pathogenic influenza A/H7N9 in Guangdong

Author

Bai, R. (Ru), Sikkema, R.S. (Reina S.), Oude Munnink, B.B. (Bas B.), Li, C.R. (Cong Rong), Wu, J. (Jie), Zou, L. (Lirong), Jing, Y. (Yi), Lu, J. (Jing), Yuan, R.Y. (Run Yu), Liao, M. (Ming), Koopmans D.V.M., M.P.G. (Marion), Ke, C.-W. (Chang-Wen), Bai, R. (Ru), Sikkema, R.S. (Reina S.), Oude Munnink, B.B. (Bas B.), Li, C.R. (Cong Rong), Wu, J. (Jie), Zou, L. (Lirong), Jing, Y. (Yi), Lu, J. (Jing), Yuan, R.Y. (Run Yu), Liao, M. (Ming), Koopmans D.V.M., M.P.G. (Marion), and Ke, C.-W. (Chang-Wen)

Abstract

The first highly pathogenic (HP) influenza A/H7N9 was reported in Guangdong in January 2017. To investigate the emergence and spread of HP A/H7N9 in Guangdong province, we sequenced 297 viruses (58 HP A/H7N9, 19 low pathogenic (LP) A/ H7N9, and 220 A/H9N2) during 2016-2017. Our analysis showed that during the fifth wave, three A/H7N9 lineages were cocirculating in Guangdong: The local LP Pearl River Delta (PRD) lineage (13%), the newly imported LP Yangtze River Delta (YRD) lineage (23%), and the HP YRD lineage (64%). Previously circulating YRD-lineage LP during the third wave evolved to the YRD-lineage HP A/H7N9 in Guangdong. All YRD-lineage LP detected during the fifth wave most likely originated from newly imported viruses into Guangdong. Genotype comparison of HP A/H7N9 suggests limited outward spread of HP A/ H7N9 to other provinces. The distribution of HP A/H7N9 cleavage site variants on live poultry markets differed from that found in humans, suggesting a V1-Type

Published
2020
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10. Ending COVID-19: progress and gaps in research-highlights of the July 2020 GloPID-R COVID-19 Research Synergies Meetings

Author

Boily-Larouche, G., Carson, G, Golding, J. (Jean), Depoortere, E., Almeida, J.R. (Jorge), Vaux, R., Paparella, G., Vitali, D., Khursigara, D., Madelaine, C., Lay, A.M., Kerstiens, B., Yazdanpanah, Y, Kaushic, C., Zaidi, A., Saville, M., Yeskey, D., Gray, G, Veloso, V., Koopmans D.V.M., M.P.G. (Marion), Fisman, D., Crooks, K., Camargo, K., Boily-Larouche, G., Carson, G, Golding, J. (Jean), Depoortere, E., Almeida, J.R. (Jorge), Vaux, R., Paparella, G., Vitali, D., Khursigara, D., Madelaine, C., Lay, A.M., Kerstiens, B., Yazdanpanah, Y, Kaushic, C., Zaidi, A., Saville, M., Yeskey, D., Gray, G, Veloso, V., Koopmans D.V.M., M.P.G. (Marion), Fisman, D., Crooks, K., and Camargo, K.

Published
2020
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11. Zika virus infection in pregnancy: a protocol for the joint analysis of the prospective cohort studies of the ZIKAlliance, ZikaPLAN and ZIKAction consortia

Author

Ades, A.E. (Anthony), Brickley, E.B. (Elizabeth B.), Alexander, N. (Neal), Brown, D. (David), Jaenisch, T. (Thomas), Miranda-Filho, D.B. (Demócrito de Barros), Pohl, M. (Moritz), Rosenberger, K.D. (Kerstin D.), Soriano-Arandes, A. (Antoni), Thorne, C. (Claire), Ximenes, R.A.A. (Ricardo Arraes de Alencar), de Araújo, T.V.B. (Thalia Velho Barreto), Avelino-Silva, V.I. (Vivian I.), Bethencourt Castillo, S.E. (Sarah Esperanza), Borja Aburto, V.H. (Victor Hugo), Brasil, P. (Patrícia), Christie, C.D.C. (Celia D C), de Souza, W.V. (Wayner Vieira), Gotuzzo H, J.E. (Jose Eduardo), Hoen, B. (Bruno), Koopmans D.V.M., M.P.G. (Marion), Martelli, C.M.T. (Celina Maria Turchi), Martins Teixeira, M. (Mauro), Marques, E.T.A. (Ernesto T A), Miranda, M.C. (Maria Consuelo), Montarroyos, U.R. (Ulisses Ramos), Moreira, M.E. (Maria Elisabeth), Morris, J.G. (J Glenn), Rockx, B. (Barry), Saba Villarroel, P.M. (Paola Mariela), Soria Segarra, C. (Carmen), Tami, A. (Adriana), Turchi, M.D. (Marília Dalva), Giaquinto, C. (Carlo), de Lamballerie, X. (Xavier), Wilder-Smith, A. (Annelies), Ades, A.E. (Anthony), Brickley, E.B. (Elizabeth B.), Alexander, N. (Neal), Brown, D. (David), Jaenisch, T. (Thomas), Miranda-Filho, D.B. (Demócrito de Barros), Pohl, M. (Moritz), Rosenberger, K.D. (Kerstin D.), Soriano-Arandes, A. (Antoni), Thorne, C. (Claire), Ximenes, R.A.A. (Ricardo Arraes de Alencar), de Araújo, T.V.B. (Thalia Velho Barreto), Avelino-Silva, V.I. (Vivian I.), Bethencourt Castillo, S.E. (Sarah Esperanza), Borja Aburto, V.H. (Victor Hugo), Brasil, P. (Patrícia), Christie, C.D.C. (Celia D C), de Souza, W.V. (Wayner Vieira), Gotuzzo H, J.E. (Jose Eduardo), Hoen, B. (Bruno), Koopmans D.V.M., M.P.G. (Marion), Martelli, C.M.T. (Celina Maria Turchi), Martins Teixeira, M. (Mauro), Marques, E.T.A. (Ernesto T A), Miranda, M.C. (Maria Consuelo), Montarroyos, U.R. (Ulisses Ramos), Moreira, M.E. (Maria Elisabeth), Morris, J.G. (J Glenn), Rockx, B. (Barry), Saba Villarroel, P.M. (Paola Mariela), Soria Segarra, C. (Carmen), Tami, A. (Adriana), Turchi, M.D. (Marília Dalva), Giaquinto, C. (Carlo), de Lamballerie, X. (Xavier), and Wilder-Smith, A. (Annelies)

Abstract

INTRODUCTION: Zika virus (ZIKV) infection in pregnancy has been associated with microcephaly and severe neurological damage to the fetus. Our aim is to document the risks of adverse pregnancy and birth outcomes and the prevalence of laboratory markers of congenital infection in deliveries to women experiencing ZIKV infection during pregnancy, using data from European Commission-funded prospective cohort studies in 20 centres in 11 countries across Latin America and the Caribbean. METHODS AND ANALYSIS: We will carry out a centre-by-centre analysis of the risks of adverse pregnancy and birth outcomes, comparing women with confirmed and suspected ZIKV infection in pregnancy to those with no evidence of infection in pregnancy. We will document the proportion of deliveries in which laboratory markers of congenital infection were present. Finally, we will investigate the associations of trimester of maternal infection in pregnancy, presence or absence of maternal symptoms of acute ZIKV infection and previous flavivirus infections with adverse outcomes and with markers of congenital infection. Centre-specific estimates will be pooled using a two-stage approach. ETHICS AND DISSEMINATION: Ethical approval was obtained at each centre. Findings will be presented at international conferences and published in peer-reviewed open access journals and discussed with local public health officials and representatives of the national Ministries of Health, Pan American Health Organization and WHO involved with ZIKV prevention and control activities.

Published
2020
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12. Increased hand hygiene compliance in nursing homes after a multimodal intervention: A cluster randomized controlled trial (HANDSOME)

Author

Teesing, G.R. (Gwen R.), Erasmus, V. (Vicky), Nieboer, D. (Daan), Petrignani, M. (Mariska), Koopmans D.V.M., M.P.G. (Marion), Vos, M.C. (Margreet C.), Verduijn-Leenman, A. (Annette), Schols, J.M.G.A. (Jos), Richardus, J.H. (Jan Hendrik), Voeten, H.A.C.M. (Hélène), Teesing, G.R. (Gwen R.), Erasmus, V. (Vicky), Nieboer, D. (Daan), Petrignani, M. (Mariska), Koopmans D.V.M., M.P.G. (Marion), Vos, M.C. (Margreet C.), Verduijn-Leenman, A. (Annette), Schols, J.M.G.A. (Jos), Richardus, J.H. (Jan Hendrik), and Voeten, H.A.C.M. (Hélène)

Abstract

Objective:To assess the effect of a multimodal intervention on hand hygiene compliance (HHC) in nursing homes.Design, setting, and participants:HHC was evaluated using direct, unobtrusive observation in a cluster randomized controlled trial at publicly funded nursing homes in the Netherlands. In total, 103 nursing home organizations were invited to participate; 18 organizations comprising 33 nursing homes (n = 66 nursing home units) participated in the study. Nursing homes were randomized into a control group (no intervention, n = 30) or an intervention group (multimodal intervention, n = 36). The primary outcome measure was HHC of nurses. HHC was appraised at baseline and at 4, 7, and 12 months after baseline. Observers and nurses were blinded.Intervention:Audits regarding hand hygiene (HH) materials and personal hygiene rules, 3 live lessons, an e-learning program, posters, and a photo contest. We used a new method to teach the nurses the WHO-defined 5 moments of HH: Room In, Room Out, Before Clean, and After Dirty.Results:HHC increased in both arms. The increase after 12 months was larger for units in the intervention arm (from 12% to 36%) than for control units (from 13% to 21%) (odds ratio [OR], 2.10; confidence interval [CI], 1.35-3.28). The intervention arm exhibited a statistically significant increase in HHC at 4 of the 5 WHO-defined HH moments. At follow-up, HHC in the intervention arm remained statistically significantly higher (OR, 1.93; 95% CI, 1.59-2.34) for indications after an activity (from 37% to 39%) than for indications before an activity (from 14% to 27%).Conclusions:The HANDSOME intervention is successful in improving HHC in nursing homes.

Published
2020
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13. Clinical and Pathological Findings in SARS-CoV-2 Disease Outbreaks in Farmed Mink (Neovison vison)

Author

Molenaar, R.J. (Robert Jan), Vreman, S. (Sandra), Hakze-van der Honing, R.W. (Renate W), Zwart, R. (Rob), de Rond, J. (Jan), Weesendorp, E. (Eefke), Smit, L.A.M., Koopmans D.V.M., M.P.G. (Marion), Bouwstra, R. (Ruth), Stegeman, A. (Arjan), Poel, W.H.M. van der, Molenaar, R.J. (Robert Jan), Vreman, S. (Sandra), Hakze-van der Honing, R.W. (Renate W), Zwart, R. (Rob), de Rond, J. (Jan), Weesendorp, E. (Eefke), Smit, L.A.M., Koopmans D.V.M., M.P.G. (Marion), Bouwstra, R. (Ruth), Stegeman, A. (Arjan), and Poel, W.H.M. van der

Abstract

SARS-CoV-2, the causative agent of COVID-19, caused respiratory disease outbreaks with increased mortality in 4 mink farms in the Netherlands. The most striking postmortem finding was an acute interstitial pneumonia, which was found in nearly all examined mink that died at the peak of the outbreaks. Acute alveolar damage was a consistent histopathological finding in mink that died with pneumonia. SARS-CoV-2 infections were confirmed by detection of viral RNA in throat swabs and by immunohistochemical detection of viral antigen in nasal conchae, trachea, and lung. Clinically, the outbreaks lasted for about 4 weeks but some animals were still polymerase chain reaction–positive for SARS-CoV-2 in throat swabs after clinical signs had disappeared. This is the first report of the clinical and pathological characteristics of SARS-CoV-2 outbreaks in mink farms.

Published
2020
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14. 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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15. Orthohantavirus Pathogenesis and Cell Tropism

Author

Noack, D. (Danny), Goeijenbier, M. (Marco), Reusken, C.B.E.M. (Chantal), Koopmans D.V.M., M.P.G. (Marion), Rockx, B. (Barry), Noack, D. (Danny), Goeijenbier, M. (Marco), Reusken, C.B.E.M. (Chantal), Koopmans D.V.M., M.P.G. (Marion), and Rockx, B. (Barry)

Abstract

Orthohantaviruses are zoonotic viruses that are naturally maintained by persistent infection in specific reservoir species. Although these viruses mainly circulate among rodents worldwide, spill-over infection to humans occurs. Orthohantavirus infection in humans can result in two distinct clinical outcomes: hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS). While both syndromes develop following respiratory transmission and are associated with multi-organ failure and high mortality rates, little is known about the mechanism

Published
2020
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16. Corrigendum: Updated classification of norovirus genogroups and genotypes

Author

Chhabra, P. (Preeti), Graaf, M. (Miranda de), Parra, G.I. (Gabriel I.), Chan, M.C.-W. (Martin Chi-Wai), Green, K. (Kim), Martella, V. (Vito), Wang, Q. (Qiuhong), White, P.A. (Peter), Katayama, K. (Kazuhiko), Vennema, H. (Harry), Koopmans D.V.M., M.P.G. (Marion), Vinjé, J. (Jan), Chhabra, P. (Preeti), Graaf, M. (Miranda de), Parra, G.I. (Gabriel I.), Chan, M.C.-W. (Martin Chi-Wai), Green, K. (Kim), Martella, V. (Vito), Wang, Q. (Qiuhong), White, P.A. (Peter), Katayama, K. (Kazuhiko), Vennema, H. (Harry), Koopmans D.V.M., M.P.G. (Marion), and Vinjé, J. (Jan)

Published
2020
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17. Spatial risk analysis for the introduction and circulation of six arboviruses in the Netherlands

Author

Esser, H.J. (Helen Joan), Liefting, Y. (Yorick), Ibáñez-Justicia, A. (Adolfo), van der Jeugd, H.P., van Turnhout, C.A.M. (Chris A M), Stroo, A. (Arjan), Reusken, C.B.E.M. (Chantal), Koopmans D.V.M., M.P.G. (Marion), de Boer, W.F. (Willem Fred), Esser, H.J. (Helen Joan), Liefting, Y. (Yorick), Ibáñez-Justicia, A. (Adolfo), van der Jeugd, H.P., van Turnhout, C.A.M. (Chris A M), Stroo, A. (Arjan), Reusken, C.B.E.M. (Chantal), Koopmans D.V.M., M.P.G. (Marion), and de Boer, W.F. (Willem Fred)

Abstract

BACKGROUND: Arboviruses are a growing public health concern in Europe, with both endemic and exotic arboviruses expected to spread further into novel areas in the next decades. Predicting where future outbreaks will occur is a major challenge, particularly for regions where these arboviruses are not endemic. Spatial modelling of ecological risk factors for arbovirus circulation can help identify areas of potential emergence. Moreover, combining hazard maps of different arboviruses may facilitate a cost-efficient, targeted multiplex-surveillance strategy in areas where virus transmission is most likely. Here, we developed predictive hazard maps for the introduction and/or establishment of six arboviruses that were previously prioritized for the Netherlands: West Nile virus, Japanese encephalitis virus, Rift Valley fever virus, tick-borne encephalitis virus, louping-ill virus and Crimean-Congo haemorrhagic fever virus. METHODS: Our spatial model included ecological risk factors that were identified as relevant for these arboviruses by an earlier systematic review, including abiotic conditions, vector abundance, and host availability. W

Published
2020
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18. Tracking echovirus eleven outbreaks in Guangdong, China

Author

Lu, J. (Jun), Kang, M. (Michelle), Zeng, H.R., Zhong, Y.W., Fang, L.Q. (Lily), Zheng, X.L., Liu, L., Yi, LN, Lin, H.F., Peng, JJ, Li, C. X., Zhang, Y.T., Sun, L.M., Luo, S.H., Xiao, J.P., Munnink, BBO, Koopmans D.V.M., M.P.G. (Marion), Wu, J., Zhang, Y., Zhang, YH, Song, T, Li, H., Zheng, H.Y., Lu, J. (Jun), Kang, M. (Michelle), Zeng, H.R., Zhong, Y.W., Fang, L.Q. (Lily), Zheng, X.L., Liu, L., Yi, LN, Lin, H.F., Peng, JJ, Li, C. X., Zhang, Y.T., Sun, L.M., Luo, S.H., Xiao, J.P., Munnink, BBO, Koopmans D.V.M., M.P.G. (Marion), Wu, J., Zhang, Y., Zhang, YH, Song, T, Li, H., and Zheng, H.Y.

Abstract

In April 2019, a suspect cluster of enterovirus cases was reported in a neonatology department in Guangdong, China, resulting in five deaths. We aimed to investigate the pathogen profiles in fatal cases, the circulation and transmission pattern of the viruses by combining metatranscriptomic, phylogenetic, and epidemiological analyses. Metatranscriptomic sequencing was used to characterize the enteroviruses. Clinical and environmental surveillance in the local population was performed to understand the prevalence and genetic diversity of the viruses in the local population. The possible source(s), evolution, transmission, and recombination of the viruses were investigated by incorporating genomes from the current outbreak, from local retrospective surveillance, and from public databases. Metatranscriptomic analysis identified Echovirus 11 (E11) in three fatal cases. Seroprevalence of neutralization antibody to E11 was 35 to 44 per cent in 3–15 age groups of general population, and the viruses were associated with various clinical symptoms. From the viral phylogeny, nosocomial transmissions were identified and all E11 2019 outbreak strains were closely related with E11 strains circulating in local population 2017–19. Frequent recombination occurred among the 2019 Guangdong E11 outbreak strains and various genotypes in enterovirus B species. This study provides an example of combining advanced genetic technology and epidemiological surveillance in pathogen diagnosis, source(s), and transmission tracing during an infectious disease outbreak. The result highlights the hidden E11 circulation and the risk of viral transmission and infection in the young age population in China. Frequent recombination between Guangdong-like strains and other enterovirus genotypes also implies the prevalence of these emerging E11 strains.

Published
2020
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19. Phenotype and kinetics of SARS-CoV-2-specific T cells in COVID-19 patients with acute respiratory distress syndrome

Author

Weiskopf, D., Schmitz, K.S., Raadsen, M.P., Grifoni, A., Okba, N.M.A. (Nisreen), Endeman, H., Akker, J.P. (Johannes) van den, Molenkamp, R., Koopmans D.V.M., M.P.G. (Marion), Gorp, E.C.M. (Eric) van, Haagmans, B.L. (Bart), Swart, R.L. (Rik) de, Sette, A. (Alessandro), Vries, R. (René) de, Weiskopf, D., Schmitz, K.S., Raadsen, M.P., Grifoni, A., Okba, N.M.A. (Nisreen), Endeman, H., Akker, J.P. (Johannes) van den, Molenkamp, R., Koopmans D.V.M., M.P.G. (Marion), Gorp, E.C.M. (Eric) van, Haagmans, B.L. (Bart), Swart, R.L. (Rik) de, Sette, A. (Alessandro), and Vries, R. (René) de

Published
2020
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20. Accelerating surveillance and research of antimicrobial resistance - an online repository for sharing of antimicrobial susceptibility data associated with whole-genome sequences

Author

Matamoros, S. (Sébastien), Hendriksen, R.S. (Rene S.), Pataki, B.Á. (Bálint Ármin), Pakseresht, N. (Nima), Rossello, M. (Marc), Silvester, N. (Nicole), Amid, C. (Clara), Aarestrup, F.M. (Frank), Koopmans D.V.M., M.P.G. (Marion), Cochrane, G. (Guy), Csabai, I. (Istvan), Lund, O. (Ole), Schultsz, C. (Constance), The Compare Ml-Amr Group, (), Matamoros, S. (Sébastien), Hendriksen, R.S. (Rene S.), Pataki, B.Á. (Bálint Ármin), Pakseresht, N. (Nima), Rossello, M. (Marc), Silvester, N. (Nicole), Amid, C. (Clara), Aarestrup, F.M. (Frank), Koopmans D.V.M., M.P.G. (Marion), Cochrane, G. (Guy), Csabai, I. (Istvan), Lund, O. (Ole), Schultsz, C. (Constance), and The Compare Ml-Amr Group, ()

Abstract

Antimicrobial resistance (AMR) is an emerging threat to modern medicine. Improved diagnostics and surveillance of resistant bacteria require the development of next-generation analysis tools and collabora

Published
2020
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21. Specialist laboratory networks as preparedness and response tool - the Emerging Viral Diseases-Expert Laboratory Network and the Chikungunya outbreak, Thailand, 2019

Author

Venturi, G., Aberle, S.W., Avsic-Zupanc, T., Barzon, L, Batejat, C., Burdino, E., Carletti, F., Charrel, R, Christova, I., Connell, J. (John), Corman, V.M. (Victor), Emmanouil, M., Jaaskelainen, A.J., Kurolt, I., Lustig, Y., Martinez, M.J., Koopmans D.V.M., M.P.G. (Marion), Nagy, O., Nguyen, T., Papa, A, Perez-Ruiz, M., Pfeffer, M., Protic, J., Reimerink, J, Rossini, G., Farinas, M., Schmidt-Chanasit, J. (Jonas), Soderholm, S., Sudre, B., Van Esbroeck, M., Reusken, C.B.E.M. (Chantal), Venturi, G., Aberle, S.W., Avsic-Zupanc, T., Barzon, L, Batejat, C., Burdino, E., Carletti, F., Charrel, R, Christova, I., Connell, J. (John), Corman, V.M. (Victor), Emmanouil, M., Jaaskelainen, A.J., Kurolt, I., Lustig, Y., Martinez, M.J., Koopmans D.V.M., M.P.G. (Marion), Nagy, O., Nguyen, T., Papa, A, Perez-Ruiz, M., Pfeffer, M., Protic, J., Reimerink, J, Rossini, G., Farinas, M., Schmidt-Chanasit, J. (Jonas), Soderholm, S., Sudre, B., Van Esbroeck, M., and Reusken, C.B.E.M. (Chantal)

Published
2020
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22. SARS-CoV-2 productively infects human gut enterocytes

Author

Lamers, M.M. (Mart M.), Beumer, J. (Joep), van der Vaart, J. (Jelte), Knoops, K. (Kèvin), Puschhof, J. (Jens), Breugem, T.I. (Tim I.), Ravelli, R.B.G. (Raimond B.), Paul van Schayck, J. (J.), Mykytyn, A.Z. (Anna Z.), Duimel, H.Q. (Hans Q.), van Donselaar, E. (Elly), Riesebosch, S. (Samra), Kuijpers, H.J.H. (Helma J H), Schipper, D. (Debby), van de Wetering, W.J. (Willine J.), Graaf, M. (Miranda) de, Koopmans D.V.M., M.P.G. (Marion), Cuppen, E. (Edwin), Peters, P.J. (Peter J.), Haagmans, B.L. (Bart), Clevers, H.C. (Hans), Lamers, M.M. (Mart M.), Beumer, J. (Joep), van der Vaart, J. (Jelte), Knoops, K. (Kèvin), Puschhof, J. (Jens), Breugem, T.I. (Tim I.), Ravelli, R.B.G. (Raimond B.), Paul van Schayck, J. (J.), Mykytyn, A.Z. (Anna Z.), Duimel, H.Q. (Hans Q.), van Donselaar, E. (Elly), Riesebosch, S. (Samra), Kuijpers, H.J.H. (Helma J H), Schipper, D. (Debby), van de Wetering, W.J. (Willine J.), Graaf, M. (Miranda) de, Koopmans D.V.M., M.P.G. (Marion), Cuppen, E. (Edwin), Peters, P.J. (Peter J.), Haagmans, B.L. (Bart), and Clevers, H.C. (Hans)

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause coronavirus disease 2019 (COVID-19), an influenza-like disease that is primarily thought to infect the lungs with transmission through the respiratory route. However, clinical evidence suggests that the intestine may present another viral target organ. Indeed, the SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) is highly expressed on differentiated enterocytes. In human small intestinal organoids (hSIOs), enterocytes were readily infected by SARS-CoV and SARS-CoV-2, as demonstrated by confocal and electron microscopy. Enterocytes produced infectious viral particles, whereas messenger RNA expression analysis of hSIOs revealed induction of a generic viral response program. Therefore, the intestinal epithelium supports SARS-CoV-2 replication, and hSIOs serve as an experimental model for coronavirus infection and biology.

Published
2020
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23. SARS-CoV-2 infection in farmed minks, the Netherlands, April and May 2020

Author

Oreshkova, N., Molenaar, R.J. (Remco), Vreman, S., Harders, F., Munnink, BBO, Hakze-van Der Honing, R.W., Gerhards, N., Tolsma, P., Bouwstra, R., Sikkema, R. S., Tacken, M.G.J., de Roolj, M.M.T., Weesendorp, E., Engelsma, M.Y., Bruschke, C.J.M., Smit, L. A. M., Koopmans D.V.M., M.P.G. (Marion), Poel, W.H.M. van der, Stegeman, A., Oreshkova, N., Molenaar, R.J. (Remco), Vreman, S., Harders, F., Munnink, BBO, Hakze-van Der Honing, R.W., Gerhards, N., Tolsma, P., Bouwstra, R., Sikkema, R. S., Tacken, M.G.J., de Roolj, M.M.T., Weesendorp, E., Engelsma, M.Y., Bruschke, C.J.M., Smit, L. A. M., Koopmans D.V.M., M.P.G. (Marion), Poel, W.H.M. van der, and Stegeman, A.

Published
2020
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24. Comparative pathogenesis of COVID-19, MERS, and SARS in a nonhuman primate model

Author

Rockx, B. (Barry), Kuiken, T. (Thijs), Herfst, S. (Sander), Bestebroer, T.M. (Theo), Lamers, MM, Munnink, BBO, Meulder, D. (Dennis) de, Amerongen, G. (Geert) van, Brand, J.M.A. (Judith) van den, Okba, N.M.A. (Nisreen), Schipper, D. (Debby), Run, P.R.W.A. (Peter) van, Leijten, L.M.E. (Lonneke), Sikkema, R., Verschoor, E., Verstrepen, B., Bogers, W., Langermans, J, Drosten, C. (Christian), van Vlissingen, M.F., Fouchier, R.A.M. (Ron), Swart, R.L. (Rik) de, Koopmans D.V.M., M.P.G. (Marion), Haagmans, B.L. (Bart), Rockx, B. (Barry), Kuiken, T. (Thijs), Herfst, S. (Sander), Bestebroer, T.M. (Theo), Lamers, MM, Munnink, BBO, Meulder, D. (Dennis) de, Amerongen, G. (Geert) van, Brand, J.M.A. (Judith) van den, Okba, N.M.A. (Nisreen), Schipper, D. (Debby), Run, P.R.W.A. (Peter) van, Leijten, L.M.E. (Lonneke), Sikkema, R., Verschoor, E., Verstrepen, B., Bogers, W., Langermans, J, Drosten, C. (Christian), van Vlissingen, M.F., Fouchier, R.A.M. (Ron), Swart, R.L. (Rik) de, Koopmans D.V.M., M.P.G. (Marion), and Haagmans, B.L. (Bart)

Published
2020
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25. 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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26. Public health response to two imported, epidemiologically related cases of Lassa fever in the Netherlands (ex Sierra Leone), November 2019

Author

Overbosch, F., Boer, M.L. (Monique) den, Veldkamp, KE, Ellerbroek, P., Bleeker-Rovers, C.P., Goorhuis, B., Vugt, M. (Mark) van, Eijck, A.A. (Annemiek), Leenstra, T, Khargi, M., Ros, J., Brandwagt, D., Haverkate, M., Swaan, C. (Corien), Reusken, C.B.E.M. (Chantal), Timen, A. (Aura), Koopmans D.V.M., M.P.G. (Marion), van Dissel, J., Overbosch, F., Boer, M.L. (Monique) den, Veldkamp, KE, Ellerbroek, P., Bleeker-Rovers, C.P., Goorhuis, B., Vugt, M. (Mark) van, Eijck, A.A. (Annemiek), Leenstra, T, Khargi, M., Ros, J., Brandwagt, D., Haverkate, M., Swaan, C. (Corien), Reusken, C.B.E.M. (Chantal), Timen, A. (Aura), Koopmans D.V.M., M.P.G. (Marion), and van Dissel, J.

Published
2020
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27. SARS-CoV-2 infection in farmed minks, the Netherlands, April and May 2020

Author

Oreshkova, N. (Nadia), Molenaar, R.J. (Robert Jan), Vreman, S. (Sandra), Harders, F. (Frank), Oude Munnink, B.B. (Bas B.), Hakze-van der Honing, R.W. (Renate W.), Gerhards, N. (Nora), Tolsma, P. (Paulien), Bouwstra, R. (Ruth), Sikkema, R.S. (Reina S.), Tacken, M.G. (Mirriam Gj), de Rooij, M.M. (Myrna Mt), Weesendorp, E. (Eefke), Engelsma, M.Y. (Marc Y.), Bruschke, C.J. (Christianne Jm), Smit, L.A. (Lidwien Am), Koopmans D.V.M., M.P.G. (Marion), Poel, W.H.M. van der, Stegeman, A. (Arjan), Oreshkova, N. (Nadia), Molenaar, R.J. (Robert Jan), Vreman, S. (Sandra), Harders, F. (Frank), Oude Munnink, B.B. (Bas B.), Hakze-van der Honing, R.W. (Renate W.), Gerhards, N. (Nora), Tolsma, P. (Paulien), Bouwstra, R. (Ruth), Sikkema, R.S. (Reina S.), Tacken, M.G. (Mirriam Gj), de Rooij, M.M. (Myrna Mt), Weesendorp, E. (Eefke), Engelsma, M.Y. (Marc Y.), Bruschke, C.J. (Christianne Jm), Smit, L.A. (Lidwien Am), Koopmans D.V.M., M.P.G. (Marion), Poel, W.H.M. van der, and Stegeman, A. (Arjan)

Abstract

Respiratory disease and increased mortality occurred in minks on two farms in the Netherlands, with interstitial pneumonia and SARS-CoV-2 RNA in organ and swab samples. On both farms, at least one worker had coronavirus disease-associated symptoms before the outbreak. Variations in mink-derived viral genomes showed between-mink transmission and no infection link between the farms. Inhalable dust contained viral RNA, indicating possible exposure of workers. One worker is assumed to have attracted the virus from mink.

Published
2020
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28. An evaluation of COVID-19 serological assays informs future diagnostics and exposure assessment

Author

Geurts van Kessel, C.H. (Corine), Okba, N.M.A. (Nisreen), Igloi, Z. (Zsofia), Bogers, S. (Susanne), Embregts, C.W.E. (Carmen W. E.), Laksono, B.M. (Brigitta), Leijten, L.M.E. (Lonneke), Rokx, C. (Casper), Rijnders, B.J.A. (Bart), Rahamat-Langendoen, J. (Janette), Van Den Akker, J.P.C., Kampen, J.J.A. (Jeroen) van, Eijck, A.A. (Annemiek), Binnendijk, R.S. (Rob) van, Haagmans, B.L. (Bart), Koopmans D.V.M., M.P.G. (Marion), Geurts van Kessel, C.H. (Corine), Okba, N.M.A. (Nisreen), Igloi, Z. (Zsofia), Bogers, S. (Susanne), Embregts, C.W.E. (Carmen W. E.), Laksono, B.M. (Brigitta), Leijten, L.M.E. (Lonneke), Rokx, C. (Casper), Rijnders, B.J.A. (Bart), Rahamat-Langendoen, J. (Janette), Van Den Akker, J.P.C., Kampen, J.J.A. (Jeroen) van, Eijck, A.A. (Annemiek), Binnendijk, R.S. (Rob) van, Haagmans, B.L. (Bart), and Koopmans D.V.M., M.P.G. (Marion)

Abstract

The world is entering a new era of the COVID-19 pandemic in which there is an increasing call for reliable antibody testing. To support decision making on the deployment of serology for either population screening or diagnostics, we present a detailed comparison of serological COVID-19 assays. We show that among the selected assays there is a wide diversity in assay performance in different scenarios and when correlated to virus neutralizing antibodies. The Wantai ELISA detecting total immunoglobulins against the receptor binding domain of SARS CoV-2, has the best overall characteristics to detect functional antibodies in different stages and severity of disease, including the potential to set a cut-off indicating the presence of protective antibodies. The large variety of available serological assays requires proper assay validation before deciding on deployment of assays for specific applications.

Published
2020
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29. SARS-CoV-2 is transmitted via contact and via the air between ferrets

Author

Richard, M. (Mathilde), Kok, A. (Adinda), Meulder, D. (Dennis) de, Bestebroer, T.M. (Theo), Lamers, M.M. (Mart M.), Okba, N.M.A. (Nisreen), Fentener van Vlissingen, M. (Martje), Rockx, B. (Barry), Haagmans, B.L. (Bart), Koopmans D.V.M., M.P.G. (Marion), Fouchier, R.A.M. (Ron), Herfst, S. (Sander), Richard, M. (Mathilde), Kok, A. (Adinda), Meulder, D. (Dennis) de, Bestebroer, T.M. (Theo), Lamers, M.M. (Mart M.), Okba, N.M.A. (Nisreen), Fentener van Vlissingen, M. (Martje), Rockx, B. (Barry), Haagmans, B.L. (Bart), Koopmans D.V.M., M.P.G. (Marion), Fouchier, R.A.M. (Ron), and Herfst, S. (Sander)

Abstract

SARS-CoV-2, a coronavirus that emerged in late 2019, has spread rapidly worldwide, and information about the modes of transmission of SARS-CoV-2 among humans is critical to apply appropriate infection control measures and to slow its spread. Here we show that SARS-CoV-2 is transmitted efficiently via direct contact and via the air (via respiratory droplets and/or aerosols) between ferrets, 1 to 3 days and 3 to 7 days after exposure respectively. The pattern of virus shedding in the direct contact and indirect recipient ferrets is similar to that of the inoculated ferrets and infectious virus is isolated from all positive animals, showing that ferrets are productively infected via either route. This study provides experimental evidence of robust transmission of SARS-CoV-2 via the air, supporting the implementation of community-level social distancing measures currently applied in many countries in the world and informing decisions on infection control measures in healthcare settings.

Published
2020
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30. Rapid assessment of regional SARS-CoV-2 community transmission through a convenience sample of healthcare workers, the Netherlands, March 2020

Author

Reusken, C.B.E.M. (Chantal), Buiting, A.G.M. (Anton), Bleeker-Rovers, C.P. (Chantal P.), Diederen, B.M.W. (Bram), Hooiveld, M.J.J., Friesema, I.H.M., Koopmans D.V.M., M.P.G. (Marion), Kortbeek, T. (Titia), Lutgens, S.P.M. (Suzanne P.), Meijer, A. (Adam), Murk, J.L. (J.), Overdevest, I. (Ilse), Trienekens, T. (Thera), Timen, A. (Aura), van den Bijllaardt, W. (Wouter), Dissel, J.T. (Jaap) van, Gageldonk-Lafeber, A.B. (Rianne) van, Van Der Vegt, D. (Dewi), Wever, P.C. (Peter C.), Hoek, W. (Wim) van der, Kluytmans, J.A.J.W. (Jan), Reusken, C.B.E.M. (Chantal), Buiting, A.G.M. (Anton), Bleeker-Rovers, C.P. (Chantal P.), Diederen, B.M.W. (Bram), Hooiveld, M.J.J., Friesema, I.H.M., Koopmans D.V.M., M.P.G. (Marion), Kortbeek, T. (Titia), Lutgens, S.P.M. (Suzanne P.), Meijer, A. (Adam), Murk, J.L. (J.), Overdevest, I. (Ilse), Trienekens, T. (Thera), Timen, A. (Aura), van den Bijllaardt, W. (Wouter), Dissel, J.T. (Jaap) van, Gageldonk-Lafeber, A.B. (Rianne) van, Van Der Vegt, D. (Dewi), Wever, P.C. (Peter C.), Hoek, W. (Wim) van der, and Kluytmans, J.A.J.W. (Jan)

Abstract

To rapidly assess possible community transmission in Noord-Brabant, the Netherlands, healthcare workers (HCW) with mild respiratory complaints and without epidemiological link (contact with confirmed case or visited areas with active c

Published
2020
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31. 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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32. Shedding of yellow fever virus from an imported case in the Netherlands after travel to Brazil

Author

Phan, M.V.T. (My V.T.), Melo, M.M. (Mariana Mendonca), van Nood, E., Aron, G.I. (Georgina), Kreeft-Voermans, J.J.C. (Jolanda J.C.), Koopmans D.V.M., M.P.G. (Marion), Reusken, C.B.E.M. (Chantal), Kessel, C.H.G. (Corine H. Geurtsvan), Cotten, M. (Matthew), Phan, M.V.T. (My V.T.), Melo, M.M. (Mariana Mendonca), van Nood, E., Aron, G.I. (Georgina), Kreeft-Voermans, J.J.C. (Jolanda J.C.), Koopmans D.V.M., M.P.G. (Marion), Reusken, C.B.E.M. (Chantal), Kessel, C.H.G. (Corine H. Geurtsvan), and Cotten, M. (Matthew)

Abstract

We report yellow fever infection in a Dutch traveler returning from Brazil. Yellow fever virus (YFV) was identified in serum and urine samples over a period of 1 month. Yellow fever virus genome sequences from the patient clustered with recent Brazilian YFV and showed with limited nucleotide changes during the resolving infection.

Published
2020
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33. Improving hand hygiene compliance in nursing homes: Protocol for a cluster randomized controlled trial (HANDSOME Study)

Author

Teesing, G.R. (Gwen R.), Erasmus, V. (Vicky), Petrignani, M. (Mariska), Koopmans D.V.M., M.P.G. (Marion), Graaf, M. (Miranda) de, Vos, M.C. (Margreet C.), Klaassen, C.H.W. (Corné H.W.), Verduijn-Leenman, A. (Annette), Schols, J.M.G.A. (Jos), Richardus, J.H. (Jan Hendrik), Voeten, H.A.C.M. (Hélène), Teesing, G.R. (Gwen R.), Erasmus, V. (Vicky), Petrignani, M. (Mariska), Koopmans D.V.M., M.P.G. (Marion), Graaf, M. (Miranda) de, Vos, M.C. (Margreet C.), Klaassen, C.H.W. (Corné H.W.), Verduijn-Leenman, A. (Annette), Schols, J.M.G.A. (Jos), Richardus, J.H. (Jan Hendrik), and Voeten, H.A.C.M. (Hélène)

Abstract

Background: Hand hygiene compliance is considered the most (cost-)effective measure for preventing health care-associated infections. While hand hygiene interventions have frequently been implemented and assessed in hospitals, there is limited knowledge about hand hygiene compliance in other health care settings and which interventions and implementation methods are effective. Objective: This study aims to evaluate the effect of a multimodal intervention to increase hand hygiene compliance of nurses in nursing homes through a cluster randomized controlled trial (HANDSOME study). Methods: Nursing homes were randomly allocated to 1 of 3 trial arms: Receiving the intervention at a predetermined date, receiving the identical intervention after an infectious disease outbreak, or serving as a control arm. Hand hygiene was evaluated in nursing homes by direct observation at 4 timepoints. We documented compliance with the World Health Organization's 5 moments of hand hygiene, specifically before touching a patient, before a clean/aseptic procedure, after body fluid exposure risk, after touching a patient, and after touching patient surroundings. The primary outcome is hand hygiene compliance of the nurses to the standards of the World Health Organization. The secondary outcome is infectious disease incidence among residents. Infectious disease incidence was documented by a staff member at each nursing home unit. Outcomes will be compared with the presence of norovirus, rhinovirus, and Escherichia coli on surfaces in the nursing homes, as measured using quantitative polymerase chain reaction. Results: The study was funded in September 2015. Data collection started in October 20

Published
2020
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34. Prevalence and Clinical Presentation of Health Care Workers With Symptoms of Coronavirus Disease 2019 in 2 Dutch Hospitals During an Early Phase of the Pandemic

Author

Kluytmans-Vandenbergh, M.F.Q. (Marjolein), Buiting, A.G.M. (Anton), Pas, S.D. (Suzan), Bentvelsen, R.G. (Robbert G.), van den Bijllaardt, W. (Wouter), van Oudheusden, A.J.G. (Anne J G), van Rijen, M.M.L. (Miranda M L), Verweij, J.J. (Jaco J.), Koopmans D.V.M., M.P.G. (Marion), Kluytmans, J.A.J.W. (Jan), Kluytmans-Vandenbergh, M.F.Q. (Marjolein), Buiting, A.G.M. (Anton), Pas, S.D. (Suzan), Bentvelsen, R.G. (Robbert G.), van den Bijllaardt, W. (Wouter), van Oudheusden, A.J.G. (Anne J G), van Rijen, M.M.L. (Miranda M L), Verweij, J.J. (Jaco J.), Koopmans D.V.M., M.P.G. (Marion), and Kluytmans, J.A.J.W. (Jan)

Abstract

Importance: On February 27, 2020, the first patient with coronavirus disease 2019 (COVID-19) was reported in the Netherlands. During the following weeks, at 2 Dutch teaching hospitals, 9 health care workers (HCWs) received a diagnosis of COVID-19, 8 of whom had no history of travel to China or northern Italy, raising the question of whether undetected community circulation was occurring. Objective: To determine the prevalence and clinical presentation of COVID-19 among HCWs with self-reported fever or respiratory symptoms. Design, Setting, and Participants: This cross-sectional study was performed in 2 teaching hospitals in the southern part of the Netherlands in March 2020, during the early phase of the COVID-19 pandemic. Health care workers employed in the participating hospitals who experienced fever or respiratory symptoms were asked to voluntarily participate in a screening for infection with the severe acute respiratory syndrome coronavirus 2. Data analysis was performed in March 2020. Main Outcomes and Measures: The prevalence of severe acute respiratory syndrome coronavirus 2 infection was determined by semiquantitative real-time reverse transcriptase-polymerase chain reaction on oropharyngeal samples. Structured interviews were conducted to document symptoms for all HCWs with confirmed COVID-19. Results: Of 9705 HCWs employed (1722 male [18%]), 1353 (14%) reported fever or respiratory symptoms and were tested. Of those, 86 HCWs (6%) were infected with severe acute respiratory syndrome coronavirus 2 (median age, 49 years [range, 22-66 years]; 15 [17%] male), representing 1% of all HCWs employed. Most HCWs experienced mild disease, and only 46 (53%) reported fever. Eighty HCWs (93%) met a case definition of fever and/or coughing and/or shortness of breath. Only 3 (3%) of the HCWs identified through the screening had a history of travel to China or northern Italy, and 3 (3%) reported having been exposed to an inpatient with a known diagnosis of COVID-19 before

Published
2020
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35. First molecular analysis of rabies virus in Qatar and clinical cases imported into Qatar, a case report

Author

Oude Munnink, B.B. (Bas B.), Farag, E.A.B.A. (Elmoubashar Abu Baker Abd), Geurts van Kessel, C.H. (Corine), Schapendonk, C.M.E. (Claudia), Linden, A. van der, Kohl, R.H.G., Arron, G.I. (Georgina), Ziglam, H. (Hisham), Goravey, W.G.M. (Wael Goravey Mhjoop), Coyle, P.V. (Peter V.), Ibrahim, I. (Imad), Mohran, K.A. (Khaled A.), Alrajhi, M.M.S. (Muneera Mohammed Saleh), Islam, M.M. (Md Mazharul), Abdeen, R. (Randa), Al-Zeyara, A.A.M.A.H. (A. Aziz Mahmoud A.H.), Younis, N.M. (Nidal Mahmoud), Al Romaihi, H.E. (Hamad), Thani, M.H.J.A. (Mohammad Hamad J. Al), Molenkamp, R. (Richard), Sikkema, R.S. (Reina S.), Koopmans D.V.M., M.P.G. (Marion), Oude Munnink, B.B. (Bas B.), Farag, E.A.B.A. (Elmoubashar Abu Baker Abd), Geurts van Kessel, C.H. (Corine), Schapendonk, C.M.E. (Claudia), Linden, A. van der, Kohl, R.H.G., Arron, G.I. (Georgina), Ziglam, H. (Hisham), Goravey, W.G.M. (Wael Goravey Mhjoop), Coyle, P.V. (Peter V.), Ibrahim, I. (Imad), Mohran, K.A. (Khaled A.), Alrajhi, M.M.S. (Muneera Mohammed Saleh), Islam, M.M. (Md Mazharul), Abdeen, R. (Randa), Al-Zeyara, A.A.M.A.H. (A. Aziz Mahmoud A.H.), Younis, N.M. (Nidal Mahmoud), Al Romaihi, H.E. (Hamad), Thani, M.H.J.A. (Mohammad Hamad J. Al), Molenkamp, R. (Richard), Sikkema, R.S. (Reina S.), and Koopmans D.V.M., M.P.G. (Marion)

Abstract

Identifying the origin of the rabies virus (RABV) infection may have significant implications for control measures. Here, we identified the source of a RABV infection of two Nepalese migrants in Qatar by comparing their RABV genomes with RABV genomes isolated from the brains of a RABV infected camel and fox from Qatar.

Published
2020
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36. Authors' response: Plenty of coronaviruses but no SARS-CoV-2

Author

Reusken, C.B.E.M. (Chantal), Haagmans, B.L. (Bart), Meijer, A. (Adam), Corman, V.M. (Victor), Papa, A. (Anna), Charrel, R. (Remi), Drosten, C. (Christian), Koopmans D.V.M., M.P.G. (Marion), Reusken, C.B.E.M. (Chantal), Haagmans, B.L. (Bart), Meijer, A. (Adam), Corman, V.M. (Victor), Papa, A. (Anna), Charrel, R. (Remi), Drosten, C. (Christian), and Koopmans D.V.M., M.P.G. (Marion)

Published
2020
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38. Publisher Correction: Specific memory B cell response in humans upon infection with highly pathogenic H7N7 avian influenza virus (Scientific Reports, (2020), 10, 1, (3152), 10.1038/s41598-020-60048-9)

Author

Westerhuis, B. (Brenda), ten Hulscher, H.I. (Hinke I.), Jacobi, R. (Ronald), van Beek, J. (Josine), Koopmans D.V.M., M.P.G. (Marion), Rimmelzwaan, G.F. (Guus), Meijer, A. (Adam), Binnendijk, R.S. (Rob) van, Westerhuis, B. (Brenda), ten Hulscher, H.I. (Hinke I.), Jacobi, R. (Ronald), van Beek, J. (Josine), Koopmans D.V.M., M.P.G. (Marion), Rimmelzwaan, G.F. (Guus), Meijer, A. (Adam), and Binnendijk, R.S. (Rob) van

Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020
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39. Publisher Correction: Differences in antigenic sites and other functional regions between genotype A and G mumps virus surface proteins (Scientific Reports, (2018), 8, 1, (13337), 10.1038/s41598-018-31630-z)

Author

Gouma, S. (Sigrid), Vermeire, T. (Tessa), Van Gucht, S. (Steven), Martens, L. (Lennart), Hutse, V. (Veronik), Cremer, J., Rota, P.A. (Paul), Leroux-Roels, G. (Geert), Koopmans D.V.M., M.P.G. (Marion), Binnendijk, R.S. (Rob) van, Vandermarliere, E. (Elien), Gouma, S. (Sigrid), Vermeire, T. (Tessa), Van Gucht, S. (Steven), Martens, L. (Lennart), Hutse, V. (Veronik), Cremer, J., Rota, P.A. (Paul), Leroux-Roels, G. (Geert), Koopmans D.V.M., M.P.G. (Marion), Binnendijk, R.S. (Rob) van, and Vandermarliere, E. (Elien)

Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020
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40. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

Author

Corman, V.M. (Victor), Landt, O., Kaiser, M. (Marco), Molenkamp, R. (Richard), Meijer, A. (Adam), Chu, D.K. (Daniel Kw), Bleicker, T., Brunink, S. (Sebastian), Schneider, J. (Julia), Schmidt, M.L. (Marie Luisa), Mulders, D.G. (Daphne Gjc), Haagmans, B.L. (Bart), Veer, B. (Bas) van der, van den Brink, S. (Sharon), Wijsman, L. (Lisa), Goderski, G. (Gabriel), Romette, J.-L. (Jean-Louis), Ellis, J. (Joanna), Zambon, M.C. (Maria), Peiris, M. (Malik), Goossens, H., Reusken, C.B.E.M. (Chantal), Koopmans D.V.M., M.P.G. (Marion), Drosten, C. (Christian), Corman, V.M. (Victor), Landt, O., Kaiser, M. (Marco), Molenkamp, R. (Richard), Meijer, A. (Adam), Chu, D.K. (Daniel Kw), Bleicker, T., Brunink, S. (Sebastian), Schneider, J. (Julia), Schmidt, M.L. (Marie Luisa), Mulders, D.G. (Daphne Gjc), Haagmans, B.L. (Bart), Veer, B. (Bas) van der, van den Brink, S. (Sharon), Wijsman, L. (Lisa), Goderski, G. (Gabriel), Romette, J.-L. (Jean-Louis), Ellis, J. (Joanna), Zambon, M.C. (Maria), Peiris, M. (Malik), Goossens, H., Reusken, C.B.E.M. (Chantal), Koopmans D.V.M., M.P.G. (Marion), and Drosten, C. (Christian)

Abstract

BackgroundThe ongoing outbreak of the recently emerged novel coronavirus (2019-nCoV) poses a challenge for public health laboratories as virus isolates are unavailable while there is growing evidence that the outbreak is more widespread than initially thought, and international spread through travellers does already occur.AimWe aimed to develop and deploy robust diagnostic methodology for use in public health laboratory settings without having virus material available.MethodsHere we present a validated diagnostic workflow for 2019-nCoV, its design relying on close genetic relatedness of 2019-nCoV with SARS coronavirus, making use of synthetic nucleic acid technology.ResultsThe workflow reliably detects 2019-nCoV, and further discriminates 2019-nCoV from SARS-CoV. Through coordination between academic and public laboratories, we confirmed assay exclusivity based on 297 original clinical specimens containing a full spectrum of human respiratory viruses. Control material is made available through European Virus Archive - Global (EVAg), a European Union infrastructure project.ConclusionThe present study demonstrates the enormous response capacity achieved through coordination of academic and public laboratories in national and European research networks.

Published
2020
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41. Proficiency testing of virus diagnostics based on bioinformatics analysis of simulated in silico high-throughput sequencing data sets

Author

Brinkmann, A. (Annika), Andrusch, A. (Andreas), Belka, A. (Ariane), Wylezich, C. (Claudia), Höper, D. (Dirk), Pohlmann, A. (Anne), Petersen, T.N. (Thomas Nordahl), Lucas, P. (Pierrick), Blanchard, Y. (Yannick), Papa, A. (Anna), Melidou, A. (Angeliki), Oude Munnink, B.B. (Bas B.), Matthijnssens, J. (Jelle), Deboutte, W. (Ward), Ellis, R.J. (Richard J.), Hansmann, F. (Florian), Baumgärtner, V. (Volkmar), Vries, E. (Erhard) van der, Osterhaus, A. (Albert), Camma, C. (Cesare), Mangone, I. (Iolanda), Lorusso, A. (Alessio), Marcacci, M. (Maurilia), Nunes, A. (Alexandra), Pinto, M. (Miguel), Borges, V. (Vítor), Kroneman, A. (Annelies), Schmitz, D. (Dennis), Corman, V.M. (Victor), Drosten, C. (Christian), Jones, T. (Terry), Hendriksen, R.S. (Rene S.), Aarestrup, F.M. (Frank), Koopmans D.V.M., M.P.G. (Marion), Beer, M. (Martin), Nitsche, A., Brinkmann, A. (Annika), Andrusch, A. (Andreas), Belka, A. (Ariane), Wylezich, C. (Claudia), Höper, D. (Dirk), Pohlmann, A. (Anne), Petersen, T.N. (Thomas Nordahl), Lucas, P. (Pierrick), Blanchard, Y. (Yannick), Papa, A. (Anna), Melidou, A. (Angeliki), Oude Munnink, B.B. (Bas B.), Matthijnssens, J. (Jelle), Deboutte, W. (Ward), Ellis, R.J. (Richard J.), Hansmann, F. (Florian), Baumgärtner, V. (Volkmar), Vries, E. (Erhard) van der, Osterhaus, A. (Albert), Camma, C. (Cesare), Mangone, I. (Iolanda), Lorusso, A. (Alessio), Marcacci, M. (Maurilia), Nunes, A. (Alexandra), Pinto, M. (Miguel), Borges, V. (Vítor), Kroneman, A. (Annelies), Schmitz, D. (Dennis), Corman, V.M. (Victor), Drosten, C. (Christian), Jones, T. (Terry), Hendriksen, R.S. (Rene S.), Aarestrup, F.M. (Frank), Koopmans D.V.M., M.P.G. (Marion), Beer, M. (Martin), and Nitsche, A.

Abstract

Quality management and independent assessment of high-throughput sequencing-based virus diagnostics have not yet been established as a mandatory approach for ensuring comparable results. The sensitivity and specificity of viral high-throughput sequence data analysis are highly affected by bioinformatics processing using publicly available and custom tools and databases and thus differ widely between individuals and institutions. Here we present the results of the COMPARE [Collaborative Management Platform for Detection and Analyses of (Re-) emerging and Foodborne Outbreaks in Europe] in silico virus proficiency test. An artificial, simulated in silico data set of Illumina HiSeq sequences was provided to 13 different European institutes for bioinformatics analysis to identify viral pathogens in high-throughput sequence data. Comparison of the participants’ analyses shows that the use of different tools, programs, and databases for bioinformatics analyses can impact the correct identification of viral sequences from a simple data set. The identification of slightly mutated and highly divergent virus genomes has been shown to be most challenging. Furthermore, the interpretation of the results, together with a fictitious case report, by the participants showed that in addition to the bioinformatics analysis, the virological evaluation of the results can be important in clinical settings. External quality assessment and proficiency testing should become an important part of validating high-throughput sequencing-based virus diagnostics and could improve the harmonization, comparability, and reproducibility of results. There is a need for the establishment of international proficiency testing, like that established for conventional laboratory tests such as PCR, for bioinformatics pipelines and the interpretation of such results.

Published
2019
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42. Study protocol for the multicentre cohorts of Zika virus infection in pregnant women, infants, and acute clinical cases in Latin America and the Caribbean: The ZIKAlliance consortium

Author

Avelino-Silva, V.I. (Vivian I.), Mayaud, P. (Philippe), Tami, A. (Adriana), Miranda, M.C. (Maria C.), Rosenberger, K.D. (Kerstin D.), Alexander, N. (Neal), Nacul, L. (Luis), Segurado, A. (Aluisio), Pohl, M. (Moritz), Bethencourt, S. (Sarah), Villar, L.A. (Luis A.), Viana, I.F.T. (Isabelle F. T.), Rabello, R. (Renata), Soria, C. (Carmen), Salgado, S.P. (Silvia P.), Gotuzzo, E. (Eduardo), Guzmán, M.G. (María G.), Martínez, P.A. (Pedro A.), López-Gatell, H. (Hugo), Hegewisch-Taylor, J. (Jennifer), Borja-Aburto, V.H. (Victor H.), Gonzalez, C. (Cesar), Netto, E.M. (Eduardo M.), Saba Villarroel, P.M. (Paola M.), Hoen, B. (Bruno), Brasil, P. (Patrícia), Marques, E.T.A. (Ernesto T. A.), Rockx, B. (Barry), Koopmans, M. (Marion), de Lamballerie, X. (Xavier), Jaenisch, T. (Thomas), Morales, I. (Ivonne), Tobian, F. (Frank), Uhlmann, L. (Lorenz), Schretzmann, J. (Julius), Leege, A. (Annika), Lins, R.D. (Roberto D.), De Filippis, A.M.B. (Ana Maria Bispo), Duarte, A.C.M. (Ana Claudia Machado), De Melo Espíndola, O. (Otavio), Bonaldo, M. (Myrna), Damasceno, L. (Luana), Avelino-Silva, V. (Vivian), Sabino, E. (Ester), Mendes-Correa, M.C. (Maria Cassia), Netto, E.M. (Eduardo Martins), Falcon, C. (Cristel), Rodríguez, E. (Egri), Matos, V. (Victmar), Tinedo, M.J. (Maria José), La Rosa, Y. (Yenifer), Murillo, M. (Marianela), Villar, L.A. (Luis Angel), Miranda, M.C. (Maria Consuelo), Lozano, A. (Anyela), Herrera, V.M. (Victor Mauricio), Gomez, A. (Adriana), Gelvez, R.M. (Rosa Margarita), Ortiz, R. (Ricardo), Dimitrakis, L. (Lady), Salgado, S.P. (Silvia Paola), Arrata, M.R. (Mary Regato), Allison, H.G. (Humberto Guerra), Talledo, M. (Michael), Villarroel, P.M.S. (Paola Mariela Saba), Torres, E.M. (Eric Martínez), Martínez Rodríguez, P.A. (Pedro A.), Vera, M.A. (Mayling Alvarez), Santana, B.G. (Belkis Galindo), Reyes, A. (Alicia), Álvarez, S.S. (Silvia Serrano), Dorticós, D.F. (Diana Ferriol), Alpuche-Aranda, C. (Celia), González-Diaz, E. (Esteban), Pavía-Ruz, N. (Norma), Borja-Aburto, V.H. (Victor Hugo), Grajales, C. (Concepción), Rojas, T. (Teresita), Arriaga, L. (Lumumba), Vallejos, A. (Alfonso), Tynevez, D. (Dominique), De Lamballerie, X. (Xavier), Thirion, L. (Laurence), Drexler, J.-F. (Jan-Felix), Gorp, E.C.M. (Eric) van, Koopmans D.V.M., M.P.G. (Marion), Avelino-Silva, V.I. (Vivian I.), Mayaud, P. (Philippe), Tami, A. (Adriana), Miranda, M.C. (Maria C.), Rosenberger, K.D. (Kerstin D.), Alexander, N. (Neal), Nacul, L. (Luis), Segurado, A. (Aluisio), Pohl, M. (Moritz), Bethencourt, S. (Sarah), Villar, L.A. (Luis A.), Viana, I.F.T. (Isabelle F. T.), Rabello, R. (Renata), Soria, C. (Carmen), Salgado, S.P. (Silvia P.), Gotuzzo, E. (Eduardo), Guzmán, M.G. (María G.), Martínez, P.A. (Pedro A.), López-Gatell, H. (Hugo), Hegewisch-Taylor, J. (Jennifer), Borja-Aburto, V.H. (Victor H.), Gonzalez, C. (Cesar), Netto, E.M. (Eduardo M.), Saba Villarroel, P.M. (Paola M.), Hoen, B. (Bruno), Brasil, P. (Patrícia), Marques, E.T.A. (Ernesto T. A.), Rockx, B. (Barry), Koopmans, M. (Marion), de Lamballerie, X. (Xavier), Jaenisch, T. (Thomas), Morales, I. (Ivonne), Tobian, F. (Frank), Uhlmann, L. (Lorenz), Schretzmann, J. (Julius), Leege, A. (Annika), Lins, R.D. (Roberto D.), De Filippis, A.M.B. (Ana Maria Bispo), Duarte, A.C.M. (Ana Claudia Machado), De Melo Espíndola, O. (Otavio), Bonaldo, M. (Myrna), Damasceno, L. (Luana), Avelino-Silva, V. (Vivian), Sabino, E. (Ester), Mendes-Correa, M.C. (Maria Cassia), Netto, E.M. (Eduardo Martins), Falcon, C. (Cristel), Rodríguez, E. (Egri), Matos, V. (Victmar), Tinedo, M.J. (Maria José), La Rosa, Y. (Yenifer), Murillo, M. (Marianela), Villar, L.A. (Luis Angel), Miranda, M.C. (Maria Consuelo), Lozano, A. (Anyela), Herrera, V.M. (Victor Mauricio), Gomez, A. (Adriana), Gelvez, R.M. (Rosa Margarita), Ortiz, R. (Ricardo), Dimitrakis, L. (Lady), Salgado, S.P. (Silvia Paola), Arrata, M.R. (Mary Regato), Allison, H.G. (Humberto Guerra), Talledo, M. (Michael), Villarroel, P.M.S. (Paola Mariela Saba), Torres, E.M. (Eric Martínez), Martínez Rodríguez, P.A. (Pedro A.), Vera, M.A. (Mayling Alvarez), Santana, B.G. (Belkis Galindo), Reyes, A. (Alicia), Álvarez, S.S. (Silvia Serrano), Dorticós, D.F. (Diana Ferriol), Alpuche-Aranda, C. (Celia), González-Diaz, E. (Esteban), Pavía-Ruz, N. (Norma), Borja-Aburto, V.H. (Victor Hugo), Grajales, C. (Concepción), Rojas, T. (Teresita), Arriaga, L. (Lumumba), Vallejos, A. (Alfonso), Tynevez, D. (Dominique), De Lamballerie, X. (Xavier), Thirion, L. (Laurence), Drexler, J.-F. (Jan-Felix), Gorp, E.C.M. (Eric) van, and Koopmans D.V.M., M.P.G. (Marion)

Abstract

Background: The European Commission (EC) Horizon 2020 (H2020)-funded ZIKAlliance Consortium designed a multicentre study including pregnant women (PW), children (CH) and natural history (NH) cohorts. Clinical sites were selected over a wide geographic range within Latin America and the Caribbean, taking into account the dynamic course of the ZIKV epidemic. Methods: Recruitment to the PW cohort will take place in antenatal care clinics. PW will be enrolled regardless of symptoms and followed over the course of pregnancy, approximately every 4 weeks. PW will be revisited at delivery (or after miscarriage/abortion) to assess birth outcomes, including microcephaly and other congenital abnormalities according to the evolving definition of congenital Zika syndrome (CZS). After birth, children will be followed for 2 years in the CH cohort. Follow-up visits are scheduled at ages 1-3, 4-6, 12, and 24 months to assess neurocognitive and developmental milestones. In addition, a NH cohort for the characterization of symptomatic rash/fever illness was designed, including follow-up to capture persisting health problems. Blood, urine, and other biological materials will be collected, and tested for ZIKV and other relevant arboviral diseases (dengue, chikungunya, yellow fever) using RT-PCR or serological methods. A virtual, decentralized biobank will be created. Reciprocal clinical monitoring has been established between partner sites. Substudies of ZIKV seroprevalence, transmission

Published
2019
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43. Zika Virus Outbreak on Curaçao and Bonaire, a Report Based on Laboratory Diagnostics Data

Author

Lim, S.M. (Stephanie), Wever, R. (Robert), Pas, S.D. (Suzan), Bonofacio, G. (Gygliola), Koopmans D.V.M., M.P.G. (Marion), Martina, B.E.E. (Byron), Lim, S.M. (Stephanie), Wever, R. (Robert), Pas, S.D. (Suzan), Bonofacio, G. (Gygliola), Koopmans D.V.M., M.P.G. (Marion), and Martina, B.E.E. (Byron)

Abstract

Background: Zika virus (ZIKV) emerged in May 2015 in Brazil, from which it spread to many other countries in Latin America. Cases of ZIKV infection were eventually also reported in Curaçao (January 2016) and Bonaire (February 2016). Methods: In the period of 16 December 2015 until 26 April 2017, serum, EDTA-plasma or urine samples were taken at Medical Laboratory Services (MLS) from patients on Curaçao and tested in qRT-PCR at the Erasmus Medical Centre (EMC) in the Netherlands. Between 17 October 2016 until 26 April 2017 all samples of suspected ZIKV-patients collected on Curaçao, as well as on Bonaire, were tested at MLS. Paired urine and/or serum samples from patients were analyzed for ZIKV shedding kinetics, and compared in terms of sensitivity for ZIKV RNA detection. Furthermore, the age and gen

Published
2019
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44. Faeces as a novel material to estimate lyssavirus prevalence in bat populations

Author

Begeman, L. (Lineke), Kooi, E.A. (Engbert A.), van Weezep, E. (Erik), Bildt, M.W.G. (Marco) van de, Reusken, C.B.E.M. (Chantal), Lina, P.H.C. (Peter H. C.), Koopmans D.V.M., M.P.G. (Marion), Brand, J.M.A. (Judith) van den, Kuiken, T. (Thijs), Begeman, L. (Lineke), Kooi, E.A. (Engbert A.), van Weezep, E. (Erik), Bildt, M.W.G. (Marco) van de, Reusken, C.B.E.M. (Chantal), Lina, P.H.C. (Peter H. C.), Koopmans D.V.M., M.P.G. (Marion), Brand, J.M.A. (Judith) van den, and Kuiken, T. (Thijs)

Abstract

Rabies is caused by infection with a lyssavirus. Bat rabies is of concern for both public health and bat conservation. The current method for lyssavirus prevalence studies in bat populations is by oral swabbing, which is invasive for the bats, dangerous for handlers, time-consuming and expensive. In many situations, such sampling is not feasible, and hence, our understanding of epidemiology of bat rabies is limited. Faeces are usually easy to collect from bat colonies without disturbing the bats and thus could be a practical and feasible material for lyssavirus prevalence studies. To further explore this idea, we performed virological analysis on faecal pellets and oral swabs of seven serotine bats (Eptesicus serotinus) that were positive for European bat 1 lyssavirus in the brain. We also performed immunohistochemical and virological analyses on digestive tract samples of these bats to determine potential sources of lyssavirus in the faeces. We found that lyssavirus detection by RT-qPCR was nearly as sensitive in faecal pellets (6/7 bats positive, 86%) as in oral swabs (7/7 bats positive, 100%). The likely source of lyssavirus in the faeces was virus excreted into the oral cavity from the salivary glands (5/6 bats positive by immunohistochemistry and RT-qPCR) or tongue (3/4 bats positive by immunohistochemistry) and swallowed with saliva. Virus could not be isolated from any of the seven faecal pellets, suggesting the lyssavirus detected in faeces is not infectious. Lyssavirus detection in the majority of faecal pellets of infected bats shows that this novel material should be further explored for lyssavirus prevalence studies in bats.

Published
2019
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45. 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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46. Metavirome Sequencing to Evaluate Norovirus Diversity in Sewage and Related Bioaccumulated Oysters

Author

Strubbia, S., Schaeffer, J., Munnink, BBO, Besnard, A., Phan, M.V.T., Nieuwenhuijse, D.F., van der Graaf, M., Schapendonk, C.M.E., Wacrenier, C., Cotten, M. (Matthew), Koopmans D.V.M., M.P.G. (Marion), le Guyader, F.S., Strubbia, S., Schaeffer, J., Munnink, BBO, Besnard, A., Phan, M.V.T., Nieuwenhuijse, D.F., van der Graaf, M., Schapendonk, C.M.E., Wacrenier, C., Cotten, M. (Matthew), Koopmans D.V.M., M.P.G. (Marion), and le Guyader, F.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 to study norovirus diversity. A double approach, agnostic deep sequencing and a capture-based approach (VirCapSeq-VERT) was used to identify norovirus in environmental samples. Family-specific viral contigs were classified and sorted by SLIM and final norovirus contigs were genotyped using the online Norovirus genotyping tool v2.0. From sewage samples, 14 norovirus genogroup I sequences were identified of which six were complete genomes. For norovirus genogroup II, nine sequences were identified and three of them comprised more than half of the genome. In oyster samples bioaccumulated with these sewage samples, only the use of an enrichment step during library preparation allowed successful identification of nine different sequences of norovirus genogroup I and four for genogroup II (>500 bp). This study demonstrates the importance of method development to increase virus recovery, and the interest of a capture-based approach to be able to identify viruses present at low concentrations.

Published
2019
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47. Worldwide human mitochondrial haplogroup distribution from urban sewage

Author

Pipek, O.A. (Orsolya Anna), Medgyes-Horváth, A. (Anna), Dobos, L. (László), Stéger, J. (József), Szalai-Gindl, J. (János), Visontai, D. (Dávid), Kaas, R.S. (Rolf S.), Koopmans D.V.M., M.P.G. (Marion), Hendriksen, R.S. (Rene S.), Aarestrup, F.M. (Frank), Csabai, I. (István), Pipek, O.A. (Orsolya Anna), Medgyes-Horváth, A. (Anna), Dobos, L. (László), Stéger, J. (József), Szalai-Gindl, J. (János), Visontai, D. (Dávid), Kaas, R.S. (Rolf S.), Koopmans D.V.M., M.P.G. (Marion), Hendriksen, R.S. (Rene S.), Aarestrup, F.M. (Frank), and Csabai, I. (István)

Abstract

Community level genetic information can be essential to direct health measures and study demographic tendencies but is subject to considerable ethical and legal challenges. These concerns become less pronounced when analyzing urban sewage samples, which are ab ovo anonymous by their pooled nature. We were able to detect traces of the human mitochondrial DNA (mtDNA) in urban sewage samples and to estimate the distribution of human mtDNA haplogroups. An expectation maximization approach was used to determine mtDNA haplogroup mixture proportions for samples collected at each different geographic location. Our results show reasonab

Published
2019
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48. 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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49. Early Measles Vaccination During an Outbreak in the Netherlands: Short-Term and Long-Term Decreases in Antibody Respo

Author

Brinkman, I.D., de Wit, J., Smits, G.P. (Gaby), ten Hulscher, HI, Jongerius, M.C., Abreu, T.C., van der Kils, F.R.M., Hahne, SJM, Koopmans D.V.M., M.P.G. (Marion), Rots, N.Y., Baarle, D. (Debbie) van, van Binnendijk, RS, Brinkman, I.D., de Wit, J., Smits, G.P. (Gaby), ten Hulscher, HI, Jongerius, M.C., Abreu, T.C., van der Kils, F.R.M., Hahne, SJM, Koopmans D.V.M., M.P.G. (Marion), Rots, N.Y., Baarle, D. (Debbie) van, and van Binnendijk, RS

Abstract

Background. The majority of infants will not be protected by maternal antibodies until their first measles vaccination, between 12 and 15 months of age. This provides incentive to reduce the age at measles vaccination, but immunological consequences are insufficiently understood, and long-term effects are largely unknown. Methods. A total of 79 infants who received early measles vaccination between 6 and 12 months age and a second dose at 14 months of age were compared to 44 children in a control group who received 1 dose at 14 months of age. Measles virus–specific neutralizing antibody concentrations and avidity were determined up to 4 years of age. Results. Infants who first received measles vaccination before 12 months of age had a long-term decrease in the concentration and avidity of measles virus–specific neutralizing antibodies, compared with infants in the control group. For 11.1% of children with a first dose before 9 months of age, antibody levels at 4 years of age had dropped below the cutoff for clinical protection. Conclusions. Early measles vaccination provides immediate protection in the majority of infants but yields a long-term decrease in neutralizing antibody responses, compared to vaccination at a later age. Additional vaccination at 14 months of age does not improve this. Over the long term, this may result in an increasing number of children susceptible to measles.

Published
2019
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50. Co-circulation of genetically distinct highly pathogenic avian influenza A clade 2.3.4.4 (H5N6) viruses in wild waterfowl and poultry in Europe and East Asia, 2017-18

Author

Poen, M.J. (Marjolein), Venkatesh, D., Bestebroer, T.M. (Theo), Vuong, O. (Oanh), Scheuer, R.D. (Rachel), Munnink, BBO, Meulder, D. (Dennis) de, Richard, M., Kuiken, T. (Thijs), Koopmans D.V.M., M.P.G. (Marion), Kelder, L., Kim, Y-J. (Yong-Jin), Lee, YJ, Steensels, M., Lambrecht, B.N.M. (Bart), Dan, A., Pohlmann, A., Beer, M. (Martin), Savic, V., Brown, I.H. (Ian), Fouchier, R.A.M. (Ron), Lewis, NS, Poen, M.J. (Marjolein), Venkatesh, D., Bestebroer, T.M. (Theo), Vuong, O. (Oanh), Scheuer, R.D. (Rachel), Munnink, BBO, Meulder, D. (Dennis) de, Richard, M., Kuiken, T. (Thijs), Koopmans D.V.M., M.P.G. (Marion), Kelder, L., Kim, Y-J. (Yong-Jin), Lee, YJ, Steensels, M., Lambrecht, B.N.M. (Bart), Dan, A., Pohlmann, A., Beer, M. (Martin), Savic, V., Brown, I.H. (Ian), Fouchier, R.A.M. (Ron), and Lewis, NS

Abstract

Highly pathogenic avian influenza (HPAI) H5 clade 2.3.4.4 viruses were first introduced into Europe in late 2014 and reintroduced in late 2016, following detections in Asia and Russia. In contrast to the 2014–15 H5N8 wave, there was substantial local virus amplification in wild birds in Europe in 2016–17 and associated wild bird mortality, with evidence for occasional gene exchange with low pathogenic avian influenza (LPAI) viruses. Since December 20

Published
2019
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