Maximum likelihood tree for cloned sequences in the E1-E2 region. The tree includes 4,184 sequences from a 406-nucleotide (nt) fragment of the E1-E2 region including hypervariable region (HVR)1 and HVR2. Sequences were obtained from patients included in the outbreak (274 patients, 3,038 sequences), patients excluded from the outbreak (47 and 559, dark purple), local controls (42 and 453, gray), and the presumed source (PS; 134 sequences, dark blue). Sequences and branches in the monophyletic clade defined by all the cloned sequences from the PS are labeled in red. Sequences from polyphyletic samples with some representatives in the clade delimited by the PS sequences and others outside it are labeled in green. Relevant nodes with bootstrap support larger than 90% are indicated by red dots. Further details can be obtained in the annotated treefile provided as Additional file 2.
González-Candelas et al. BMC Biology 2013 11:76 doi:10.1186/1741-7007-11-76