Selection of a phylogenetically informative region of the norovirus genome for outbreak linkage

Linda Verhoef*, Kelly P. Williams, Annelies Kroneman, Bruno Sobral, Wilfrid Van Pelt, Marion Koopmans

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

14 Citations (Scopus)
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Abstract

The recognition of a common source norovirus outbreak is supported by finding identical norovirus sequences in patients. Norovirus sequencing has been established in many (national) public health laboratories and academic centers, but often partial and different genome sequences are used. Therefore, agreement on a target sequence of sufficient diversity to resolve links between outbreaks is crucial. Although harmonization of laboratory methods is one of the keystone activities of networks that have the aim to identify common source norovirus outbreaks, this has proven difficult to accomplish, particularly in the international context. Here, we aimed at providing a method enabling identification of the genomic region informative of a common source norovirus outbreak by bio-informatic tools. The data set of 502 unique full length capsid gene sequences available from the public domain, combined with epidemiological data including linkage information was used to build over 3,000 maximum likelihood (ML) trees for different sequence lengths and regions. All ML trees were evaluated for robustness and specificity of clustering of known linked norovirus outbreaks against the background diversity of strains. Great differences were seen in the robustness of commonly used PCR targets for cluster detection. The capsid gene region spanning nucleotides 900-1,400 was identified as the region optimally substituting for the full length capsid region. Reliability of this approach depends on the quality of the background data set, and we recommend periodic reassessment of this growing data set. The approach may be applicable to multiple sequence-based data sets of other pathogens.

Original languageEnglish
Pages (from-to)8-18
Number of pages11
JournalVirus Genes
Volume44
Issue number1
Early online date30 Sep 2011
DOIs
Publication statusPublished - Feb 2012

Bibliographical note

Funding Information:
Acknowledgments This study was supported by the Dutch Food and Consumer Product Safety Authority, the European Commission DG Research Quality of Life Program, 6th Framework (EVENT, SP22-CT-2004-502571) and SG SANCO (DIVINE-net, 2003213). We thank Adam Meijer, Ingeborg Boxman, Erwin Duizer, Harry Vennema and Marijn van Ballegooijen for many constructive discussions that helped us to improve the manuscript.

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