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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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Sequence variation in cluster 4 of the GII.4 Den Haag 2006b variant.Seventeen sequences from cluster 4 are shown, including follow up samples from four patients with chronic NoV infection. Sequences are sorted chronologically and nucleotide positions with mixed bases and/or nucleotide changes are shown. Sequence names indicate department (Hem: hematology), sample date (mm/dd/yyyy) and eventual serial number. For patients with chronic NoV infections, a patient number is given followed by “.1” for first sample and “.2” for second sample (marked with grey background). The nucleotide position is given in relation to the reference capsid sequence from GenBank Accession Nr. EF684915.2. Period indicates the same nucleotide as in the first sample (Hem-01/28/2008).
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pone.0115331.g002: Sequence variation in cluster 4 of the GII.4 Den Haag 2006b variant.Seventeen sequences from cluster 4 are shown, including follow up samples from four patients with chronic NoV infection. Sequences are sorted chronologically and nucleotide positions with mixed bases and/or nucleotide changes are shown. Sequence names indicate department (Hem: hematology), sample date (mm/dd/yyyy) and eventual serial number. For patients with chronic NoV infections, a patient number is given followed by “.1” for first sample and “.2” for second sample (marked with grey background). The nucleotide position is given in relation to the reference capsid sequence from GenBank Accession Nr. EF684915.2. Period indicates the same nucleotide as in the first sample (Hem-01/28/2008).

Mentions: Cluster 7 represented the foodborne point source outbreak and these five sequences were identical. Four of the six hospital clusters were locally confined to one department. The three smallest clusters (3, 5 and 6) were restricted to one department each and to a period of less than one month and the sequences differed by no more than one nucleotide substitution. Thus, in these clusters the molecular epidemiology confirmed the epidemiological relation and added the information, that each of these clusters was due to a new introduction of the virus into the hospital environment. Cluster 4 included 13 samples from the hematology department over a period of 78 days. Six distinct sequence patterns differing at 12 sites (0.8%) were observed. A more detailed description of the sequence variation in this cluster, taking into account mixed bases and follow up samples from four of the patients, is given in Fig. 2 and described more detailed in the next section.


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)

Sequence variation in cluster 4 of the GII.4 Den Haag 2006b variant.Seventeen sequences from cluster 4 are shown, including follow up samples from four patients with chronic NoV infection. Sequences are sorted chronologically and nucleotide positions with mixed bases and/or nucleotide changes are shown. Sequence names indicate department (Hem: hematology), sample date (mm/dd/yyyy) and eventual serial number. For patients with chronic NoV infections, a patient number is given followed by “.1” for first sample and “.2” for second sample (marked with grey background). The nucleotide position is given in relation to the reference capsid sequence from GenBank Accession Nr. EF684915.2. Period indicates the same nucleotide as in the first sample (Hem-01/28/2008).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0115331.g002: Sequence variation in cluster 4 of the GII.4 Den Haag 2006b variant.Seventeen sequences from cluster 4 are shown, including follow up samples from four patients with chronic NoV infection. Sequences are sorted chronologically and nucleotide positions with mixed bases and/or nucleotide changes are shown. Sequence names indicate department (Hem: hematology), sample date (mm/dd/yyyy) and eventual serial number. For patients with chronic NoV infections, a patient number is given followed by “.1” for first sample and “.2” for second sample (marked with grey background). The nucleotide position is given in relation to the reference capsid sequence from GenBank Accession Nr. EF684915.2. Period indicates the same nucleotide as in the first sample (Hem-01/28/2008).
Mentions: Cluster 7 represented the foodborne point source outbreak and these five sequences were identical. Four of the six hospital clusters were locally confined to one department. The three smallest clusters (3, 5 and 6) were restricted to one department each and to a period of less than one month and the sequences differed by no more than one nucleotide substitution. Thus, in these clusters the molecular epidemiology confirmed the epidemiological relation and added the information, that each of these clusters was due to a new introduction of the virus into the hospital environment. Cluster 4 included 13 samples from the hematology department over a period of 78 days. Six distinct sequence patterns differing at 12 sites (0.8%) were observed. A more detailed description of the sequence variation in this cluster, taking into account mixed bases and follow up samples from four of the patients, is given in Fig. 2 and described more detailed in the next section.

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