Phylogenetic tree of 53 NoV genotype II.4 variant Den Haag 2006b capsid sequences.

<p>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 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0115331#pone.0115331.g004" target="_blank">Fig. 4</a>. 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.</p

Comparative phylogenetic analysis of polymerase (a.) and capsid (b.) gene sequences.

<p>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 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0115331#pone.0115331.g001" target="_blank">Fig. 1</a> (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.</p

Sequence variation in cluster 4 of the GII.4 Den Haag 2006b variant.

<p>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).</p

Local and temporal distribution of genotypes, variants and GII.4 2006b clusters.

<p>The first sample per inpatient is shown (n = 105). Units on vertical axes represent numbers of patients. NA (n = 49): no sequence information available (n = 29: sample not stored, n = 20: GII.4 specific PCR negative). The sequences from the first samples from six patients with persistent diarrhea are marked with diagonal shading.</p

Results of positive microbiological findings in water samples.

a<p>Estimations are figured with or without applying corrective factors derived by extraction efficiencies.</p>b<p>Below theoretical limit of quantification estimated at 100 genomic units/200 ml.</p><p>Results of positive microbiological findings in water samples.</p

Phylogenetic tree of NoV capsid gene sequences.

<p>Phylogenetic tree based on 11 nucleotide sequences of 1140 nt of the NoV capsid gene. All sequences are indicated by their GenBank Accession number. GenBank accession numbers used in this manuscript are from norovirus sequences from patient samples (KF798196, KF798197, KF798198 and KF798200) and water samples (KF798199 (W3) and KF798201 (W1)). The remaining norovirus sequences from patient samples used in the phylogenetic tree have been published previously <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105053#pone.0105053-Fonager1" target="_blank">[32]</a>. Legend: Circles and triangles: New Orleans 2009 variants and Squares: Sydney 2012 variants, Circles: belonging to the outbreak, Triangles: not belonging to the outbreak described here. Open triangle and square are the reference sequences for the New Orleans 2009 and Sydney 2012 variants respectively. Open circles:sequences obtained from water samples (KF798201,W1) and KF798199,W3) and closed circles are the sequences obtained from patient stool samples.</p

Attack rates (AR),relative risk (RR) and 95% confidence interval (CI) of diarrhoea and/or vomiting compared to the reference (Ref) on 12–14 December by tap-water consumption and mean daily tap-water consumption on 12–13 December, Kalundborg, Denmark.

<p>Attack rates (AR),relative risk (RR) and 95% confidence interval (CI) of diarrhoea and/or vomiting compared to the reference (Ref) on 12–14 December by tap-water consumption and mean daily tap-water consumption on 12–13 December, Kalundborg, Denmark.</p