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.