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Sequence analysis of the capsid gene during a genotype II.4 dominated norovirus season in one university hospital: identification of possible transmission routes.

Holzknecht BJ, Franck KT, Nielsen RT, Böttiger B, Fischer TK, Fonager J - PLoS ONE (2015)

Bottom Line: In addition, a more heterogeneous cluster with evidence of repeated introductions from the community, but also possible inter-department spread was observed.In all six patients with paired sequences, evidence for in vivo evolution of the virus was found.Capsid gene sequencing showed substantial sequence variation among NoV GII.4 variant Den Haag 2006b strains from one single institution during a nine months' period.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark; Department of Clinical Microbiology, Copenhagen University Hospital Herlev, Herlev, Denmark.

ABSTRACT
Norovirus (NoV) is a leading cause of gastroenteritis and genotype II.4 (GII.4) is responsible for the majority of nosocomial NoV infections. Our objective was to examine whether sequencing of the capsid gene might be a useful tool for the hospital outbreak investigation to define possible transmission routes. All NoV positive samples submitted from one university hospital during the 2007/8 season were selected. Genotyping of selected samples by partial polymerase gene sequencing had shown that the majority belonged to the GII.4 variant Den Haag 2006b and had identical polymerase sequences. Sequences of the capsid gene (1412 nucleotides) were obtained from the first available sample from 55 patients. From six immunocompromised patients with persistent infections a second sample was also included. As a control for a point-source outbreak, five samples from a foodborne outbreak caused by the same GII.4 variant were analyzed. Forty-seven of the inpatients (85%) were infected with the GII.4 variant Den Haag 2006b. Phylogenetic analysis of the Den Haag 2006b sequences identified four distinct outbreaks in different departments and a fifth outbreak with possible inter-department spread. In addition, a more heterogeneous cluster with evidence of repeated introductions from the community, but also possible inter-department spread was observed. In all six patients with paired sequences, evidence for in vivo evolution of the virus was found. Capsid gene sequencing showed substantial sequence variation among NoV GII.4 variant Den Haag 2006b strains from one single institution during a nine months' period. This method proved useful to understand the local epidemiology and, when used promptly, has the potential to make infection control measures more targeted.

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Related in: MedlinePlus

Comparative phylogenetic analysis of polymerase (a.) and capsid (b.) gene sequences.Neighbor Joining trees based on polymerase sequences (a., 226–285 nt) and capsid sequences (b., 1412 nt) of 27 samples from which both sequences were available are shown. Color labels indicate clustering according to the phylogenetic analysis of all capsid sequences shown in Fig. 1 (cluster 1: pink, cluster 2: yellow, cluster 3: brown, cluster 4: red, cluster 5: orange, foodborne cluster 7: empty black circle, singleton 2: black triangle, singleton 3: black square, singleton 4: black diamond.
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pone.0115331.g004: Comparative phylogenetic analysis of polymerase (a.) and capsid (b.) gene sequences.Neighbor Joining trees based on polymerase sequences (a., 226–285 nt) and capsid sequences (b., 1412 nt) of 27 samples from which both sequences were available are shown. Color labels indicate clustering according to the phylogenetic analysis of all capsid sequences shown in Fig. 1 (cluster 1: pink, cluster 2: yellow, cluster 3: brown, cluster 4: red, cluster 5: orange, foodborne cluster 7: empty black circle, singleton 2: black triangle, singleton 3: black square, singleton 4: black diamond.

Mentions: All capsid sequences (first sample per patient) were aligned and a Neighbor Joining tree was constructed and rooted on the branch between the Den Haag 2006b variant and the Osaka 2007 and Apeldoorn 2007 sequences. The subtree of the 2006b variant is displayed here. Sites with mixed bases were ignored for phylogenetic analysis. Sequence names represent hospital department (Hem: hematology, Neph: nephrology, IntMed1/2: internal medicine 1/2, Card: cardiology, Food: foodborne outbreak) and date of sampling (mm/dd/yyyy), eventually followed by a serial number to ensure uniqueness. Sequences from patients with symptom onset within 48 hours after hospital admission are marked with a circle (filled circle: no previous contact to hospital, empty circle: frequent contact to hospital due to hemodialysis). Sequences from the first samples from six patients with persistent diarrhea are marked with a filled triangle. Sequences from samples with an available polymerase gene sequence from previous genotyping (n = 27) are marked with asterisks and phylogenetic analysis of this subgroup is shown in Fig. 4. On the right hand side of the tree epidemiological information is given as well as numbers of nucleotide changes within the cluster and the number of distinct sequence patterns included in the cluster.


Sequence analysis of the capsid gene during a genotype II.4 dominated norovirus season in one university hospital: identification of possible transmission routes.

Holzknecht BJ, Franck KT, Nielsen RT, Böttiger B, Fischer TK, Fonager J - PLoS ONE (2015)

Comparative phylogenetic analysis of polymerase (a.) and capsid (b.) gene sequences.Neighbor Joining trees based on polymerase sequences (a., 226–285 nt) and capsid sequences (b., 1412 nt) of 27 samples from which both sequences were available are shown. Color labels indicate clustering according to the phylogenetic analysis of all capsid sequences shown in Fig. 1 (cluster 1: pink, cluster 2: yellow, cluster 3: brown, cluster 4: red, cluster 5: orange, foodborne cluster 7: empty black circle, singleton 2: black triangle, singleton 3: black square, singleton 4: black diamond.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4295850&req=5

pone.0115331.g004: Comparative phylogenetic analysis of polymerase (a.) and capsid (b.) gene sequences.Neighbor Joining trees based on polymerase sequences (a., 226–285 nt) and capsid sequences (b., 1412 nt) of 27 samples from which both sequences were available are shown. Color labels indicate clustering according to the phylogenetic analysis of all capsid sequences shown in Fig. 1 (cluster 1: pink, cluster 2: yellow, cluster 3: brown, cluster 4: red, cluster 5: orange, foodborne cluster 7: empty black circle, singleton 2: black triangle, singleton 3: black square, singleton 4: black diamond.
Mentions: All capsid sequences (first sample per patient) were aligned and a Neighbor Joining tree was constructed and rooted on the branch between the Den Haag 2006b variant and the Osaka 2007 and Apeldoorn 2007 sequences. The subtree of the 2006b variant is displayed here. Sites with mixed bases were ignored for phylogenetic analysis. Sequence names represent hospital department (Hem: hematology, Neph: nephrology, IntMed1/2: internal medicine 1/2, Card: cardiology, Food: foodborne outbreak) and date of sampling (mm/dd/yyyy), eventually followed by a serial number to ensure uniqueness. Sequences from patients with symptom onset within 48 hours after hospital admission are marked with a circle (filled circle: no previous contact to hospital, empty circle: frequent contact to hospital due to hemodialysis). Sequences from the first samples from six patients with persistent diarrhea are marked with a filled triangle. Sequences from samples with an available polymerase gene sequence from previous genotyping (n = 27) are marked with asterisks and phylogenetic analysis of this subgroup is shown in Fig. 4. On the right hand side of the tree epidemiological information is given as well as numbers of nucleotide changes within the cluster and the number of distinct sequence patterns included in the cluster.

Bottom Line: In addition, a more heterogeneous cluster with evidence of repeated introductions from the community, but also possible inter-department spread was observed.In all six patients with paired sequences, evidence for in vivo evolution of the virus was found.Capsid gene sequencing showed substantial sequence variation among NoV GII.4 variant Den Haag 2006b strains from one single institution during a nine months' period.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark; Department of Clinical Microbiology, Copenhagen University Hospital Herlev, Herlev, Denmark.

ABSTRACT
Norovirus (NoV) is a leading cause of gastroenteritis and genotype II.4 (GII.4) is responsible for the majority of nosocomial NoV infections. Our objective was to examine whether sequencing of the capsid gene might be a useful tool for the hospital outbreak investigation to define possible transmission routes. All NoV positive samples submitted from one university hospital during the 2007/8 season were selected. Genotyping of selected samples by partial polymerase gene sequencing had shown that the majority belonged to the GII.4 variant Den Haag 2006b and had identical polymerase sequences. Sequences of the capsid gene (1412 nucleotides) were obtained from the first available sample from 55 patients. From six immunocompromised patients with persistent infections a second sample was also included. As a control for a point-source outbreak, five samples from a foodborne outbreak caused by the same GII.4 variant were analyzed. Forty-seven of the inpatients (85%) were infected with the GII.4 variant Den Haag 2006b. Phylogenetic analysis of the Den Haag 2006b sequences identified four distinct outbreaks in different departments and a fifth outbreak with possible inter-department spread. In addition, a more heterogeneous cluster with evidence of repeated introductions from the community, but also possible inter-department spread was observed. In all six patients with paired sequences, evidence for in vivo evolution of the virus was found. Capsid gene sequencing showed substantial sequence variation among NoV GII.4 variant Den Haag 2006b strains from one single institution during a nine months' period. This method proved useful to understand the local epidemiology and, when used promptly, has the potential to make infection control measures more targeted.

Show MeSH
Related in: MedlinePlus