Figure 2

Phylogenetic tree displaying the genetic relationships between environmental, clinical and GenBank HAV isolates. The tree is based on a partial sequence (218 nt) of the VP1/2A junction of the HAV genome. The strains identified in this study (coded in blue or red for the years 2012 and 2013, respectively) are indicated with ID number followed by the city, month and year of sample collection. The sequence a.n. KF182323, obtained from the first case detected in Trento, is deemed to be the prototype sequence of the Italian outbreak. Still unpublished sequences from clinical cases are reported as sample ID followed by city, month and year of isolation. Other strains in the tree are shown by their GenBank accession number, strain, and year of sample collection. These include IA strains (KF182323, KF201589, KF234020, KF234021, KF182323, KF233556, KF706398, and KF706407), IB strains (DQ124883, DQ124877, AJ505624, KC876797), and one IIIA strain, KF706410, used as outgroup, to root the phylogenetic tree. The T92 (Tamura 3-parameter) model of nucleotide substitution was used, selected as the best fit model from among 24 models available in the MEGA 6.06 software. The robustness of branching patterns was tested by 1000 bootstrap pseudo-replications; bootstrap values >60 are indicated. The scale bar indicates nucleotide substitutions per site.