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

Verhoef L, Williams KP, Kroneman A, Sobral B, van Pelt W, Koopmans M, FBVE netwo - Virus Genes (2011)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: National Institute for Public Health and the Environment (RIVM), Postbak 22, 3720 BA, Bilthoven, The Netherlands. linda.verhoef@rivm.nl

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.

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Related in: MedlinePlus

Maximum likelihood tree for 502 unique full capsid gene sequences (nt positions 5,085–6,702 on the basis of X86557) from the FoodBorne Viruses in Europe database (http://www.rivm.nl/pubmpf/norovirus/database#/outbreaks/list) and Genbank. Clades are condensed (triangles) to the genotype level, assigned according to the publicly available typing tool http://www.rivm.nl/mpf/norovirus/typingtool. A nexus file is provided in electronic supplementary material 2, providing the possibility to see the tree in detail
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Fig1: Maximum likelihood tree for 502 unique full capsid gene sequences (nt positions 5,085–6,702 on the basis of X86557) from the FoodBorne Viruses in Europe database (http://www.rivm.nl/pubmpf/norovirus/database#/outbreaks/list) and Genbank. Clades are condensed (triangles) to the genotype level, assigned according to the publicly available typing tool http://www.rivm.nl/mpf/norovirus/typingtool. A nexus file is provided in electronic supplementary material 2, providing the possibility to see the tree in detail

Mentions: The alignment covered a total of 1,957 positions, with the longest sequence containing 1,677 nt. The full alignment resulted in a ML tree capable of clustering all genotypes, 10/12 variants and all outbreak events grouped together but separately from other genotypes, variants, and outbreak events (Fig. 1, of which detailed tree information in Nexus format is provided in electronic supplementary material 2).Fig. 1


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

Verhoef L, Williams KP, Kroneman A, Sobral B, van Pelt W, Koopmans M, FBVE netwo - Virus Genes (2011)

Maximum likelihood tree for 502 unique full capsid gene sequences (nt positions 5,085–6,702 on the basis of X86557) from the FoodBorne Viruses in Europe database (http://www.rivm.nl/pubmpf/norovirus/database#/outbreaks/list) and Genbank. Clades are condensed (triangles) to the genotype level, assigned according to the publicly available typing tool http://www.rivm.nl/mpf/norovirus/typingtool. A nexus file is provided in electronic supplementary material 2, providing the possibility to see the tree in detail
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3293504&req=5

Fig1: Maximum likelihood tree for 502 unique full capsid gene sequences (nt positions 5,085–6,702 on the basis of X86557) from the FoodBorne Viruses in Europe database (http://www.rivm.nl/pubmpf/norovirus/database#/outbreaks/list) and Genbank. Clades are condensed (triangles) to the genotype level, assigned according to the publicly available typing tool http://www.rivm.nl/mpf/norovirus/typingtool. A nexus file is provided in electronic supplementary material 2, providing the possibility to see the tree in detail
Mentions: The alignment covered a total of 1,957 positions, with the longest sequence containing 1,677 nt. The full alignment resulted in a ML tree capable of clustering all genotypes, 10/12 variants and all outbreak events grouped together but separately from other genotypes, variants, and outbreak events (Fig. 1, of which detailed tree information in Nexus format is provided in electronic supplementary material 2).Fig. 1

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: National Institute for Public Health and the Environment (RIVM), Postbak 22, 3720 BA, Bilthoven, The Netherlands. linda.verhoef@rivm.nl

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.

Show MeSH
Related in: MedlinePlus