Benschop, K.

Claas, E. C.

Koopmans, M.

Kroneman, A.

Niesters, H. G.

Pas, S. D.

Rahamat-Langendoen, J. C.

Schuurman, R.

van der Avoort, H.

Vennema, H.

Wolthers, K.

English

Dissertations of the University of Groningen

   University of GroningenAuthors' reply: Application of Bayesian methods to the inference of phylogeny for enterovirussurveillanceKoopmans, M.; Niesters, H. G.; Benschop, K.; Wolthers, K.; Schuurman, R.; Pas, S. D.;Claas, E. C.; Kroneman, A.; Rahamat-Langendoen, J. C.; Vennema, H.Published in:EurosurveillanceIMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite fromit. Please check the document version below.Document VersionPublisher's PDF, also known as Version of recordPublication date:2013Link to publication in University of Groningen/UMCG research databaseCitation for published version (APA):Koopmans, M., Niesters, H. G., Benschop, K., Wolthers, K., Schuurman, R., Pas, S. D., Claas, E. C.,Kroneman, A., Rahamat-Langendoen, J. C., Vennema, H., & van der Avoort, H. (2013). Authors' reply:Application of Bayesian methods to the inference of phylogeny for enterovirus surveillance.Eurosurveillance, 18(9), 21-22. [20410].CopyrightOther than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of theauthor(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license.More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne-amendment.Take-down policyIf you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediatelyand investigate your claim.Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons thenumber of authors shown on this cover page is limited to 10 maximum.1www.eurosurveillance.orgLettersAuthors’ reply: Application of Bayesian methods to the inference of phylogeny for enterovirus surveillanceM Koopmans (marion.koopmans@rivm.nl)1,2, H G Niesters3, K Benschop1,4, K Wolthers4, R Schuurman5, S D Pas2, E C Claas6,  A Kroneman1, J C Rahamat-Langendoen3, H Vennema3, H van der Avoort11. Laboratory for Infectious Diseases and Screening, Center for Infectious Diseases, National Institute of Public Health and the Environment (RIVM), Bilthoven, the Netherlands2. Department of Virology, Erasmus Medical Centre, Rotterdam, the Netherlands3. Department of Medical Microbiology, Division of Clinical Virology, University of Groningen, University Medical Center Groningen, the Netherlands4. Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands5. Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands6. Department of Medical Microbiology, Leiden University Medical Centre, Leiden, the NetherlandsCitation style for this article: Koopmans M, Niesters HG, Benschop K, Wolthers K, Schuurman R, Pas SD, Claas EC, Kroneman A, Rahamat-Langendoen JC, Vennema H, van der Avoort H. Authors’ reply: Application of Bayesian methods to the inference of phylogeny for enterovirus surveillance. Euro Surveill. 2013;18(9):pii=20410. Available online: http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=20410Article submitted on 25 February 2013 / published on 28 February 2013To the editor: We would like to thank Roberts et al. for their com-ments on our paper entitled ‘Laboratory-based surveil-lance in the molecular era: the TYPENED model, a joint data-sharing platform for clinical and public health laboratories’ [1]. We fully agree with the remarks on the potential strength of adding more advanced ana-lytical tools once the molecular surveillance network is established. In fact, this is what we have done previ-ously, as part of studies of the evolution of noroviruses and enteroviruses [2,3]. For enteroviruses, we focused those studies on enterovirus 71 (EV71), for the reasons mentioned by Roberts et al. We compared the evolu-tionary trajectory of EV71 in the Netherlands with that from a systematic collection of EV71 strains detected in southern China. This analysis showed a clear dif-ference in the circulating strains, with evidence that the EV71 subgenogroups B and C circulating in Asia have evolved further than those in Europe and the United States [3,4]. The severity of outbreaks of EV71 infection associated with the EV71 lineages circulat-ing in Asia raises the question if these viruses need to be regarded as an emerging public health problem [5].  The analysis also showed that previous peaks in reporting reflected true epidemics [3]. Further stud-ies showed that recombination was part of the driv-ing force for those epidemics [6].  We agree that such studies give a much deeper understanding of the epidemiology of enteroviruses, and would strongly support its development in an international context. The rapid transition from culture-based diagnostic methods to molecular diagnostics in clinical virology in our country was a trigger to do this, and will most likely also affect other surveillance systems such as those for influenza or food-borne bacterial pathogens [7]. However, at present, this transition has not been made in most countries globally. Our article aimed to describe the model applied in the Netherlands for an approach to molecular surveillance, in which clinical and public health laboratories collaborate by defining common goals. This model was developed to facilitate the transition, and includes comparative evaluation of surveillance trends obtained by classical and molecu-lar virological methods 1.  If outcomes are agreed upon, we will further develop the system, which would include the more advanced analytical approaches sug-gested by Roberts et al.Conflict of interestNone declared. Authors’ contributionsMarion Koopmans drafted the response letter after discus-sions and input from the authors of the article in question.References1. Niesters HG, Rossen JW, van der Avoort H, Baas D, Benschop K, Claas EC, et al. Laboratory-based surveillance in the molecular era: the TYPENED model, a joint data-sharing platform for clinical and public health laboratories. Euro Surveill. 2013;18(4):pii=20387. Available from: http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=20387 2. Siebenga JJ, Lemey P, Kosakovsky Pond SL, Rambaut A, Vennema H, Koopmans M. Phylodynamic reconstruction reveals norovirus GII.4 epidemic expansions and their molecular determinants. PLoS Pathog. 2010;6(5):e1000884. 3. van der Sanden S, van der Avoort H, Lemey P, Uslu G, Koopmans M. Evolutionary trajectory of the VP1 gene of human enterovirus 71 genogroup B and C viruses. J Gen Virol. 2010;91(Pt 8):1949-58. 4. Guan D, van der Sanden S, Zeng H, Li W, Zheng H, Ma C, et al. Population dynamics and genetic diversity of C4 strains of human enterovirus 71 in Mainland China, 1998-2010. PLoS One. 2012;7(9):e44386. 5. Solomon T, Lewthwaite P, Perera D, Cardosa MJ, McMinn P, Ooi MH. Virology, epidemiology, pathogenesis, and control of enterovirus 71. Lancet Infect Dis. 2010;10(11):778-90. http://dx.doi.org/10.1016/S1473-3099(10)70194-8 2 www.eurosurveillance.org6. van der Sanden S, van Eek J, Martin DP, van der Avoort H, Vennema H, Koopmans M. Detection of recombination breakpoints in the genomes of human enterovirus 71 strains isolated in the Netherlands in epidemic and non-epidemic years, 1963-2010.  Infect Genet Evol. 2011;11(5):886-94.  http://dx.doi.org/10.1016/j.meegid.2011.02.011 PMid:21352955 7. Jones TF, Gerner-Smidt P. Nonculture diagnostic tests for enteric diseases. Emerg Infect Dis. 2012;18(3):513-4. http://dx.doi.org/10.3201/eid1803.111914  PMid:22377326 PMCid:3309642

Authors' reply: Application of Bayesian methods to the inference of phylogeny for enterovirus surveillance

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Authors' reply: Application of Bayesian methods to the inference of phylogeny for enterovirus surveillance

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