Muhammed Babakir-Mina, Massimo Ciccozzi, Elisabetta Trento, Carlo Federico Perno, and Marco Ciotti
Figure. Unrooted phylogenetic tree showing analysis of KI (KIV-RM21, KIV-RM22) and WU (WUV-IT3) polyomaviruses (KIPyVs, WUPyVs, respectively) identified in the plasma of HIV-1–positive patients. The identified strains are indicated in boldface, and the phylogenetic analysis refers to the small t region. The other polyomaviruses shown in the figure are the KIPyVs (KIV-RM1 to KIV-RM20) and WUPyVs (WUV-IT1 and WUV-IT2) identified in Italy in previous studies (6,7) and the prototype strains for KIPyV (GenBank accession nos. EF127906, EF127908, EF520288) and WUPyV (GenBank accession nos. EF444549–EF444554, EU711054–EU711058, EU296475, EU358768, and EU358769). GenBank accession numbers for all virus strains are shown in parentheses. Multiple nucleotide sequence alignments were performed by using ClustalX software (http://bips.u-strasbg.fr/fr/documentation/clustalx/#g), and the phylogenetic tree was constructed by using the neighbor-joining algorithm with LogDet-corrected distances (http://paup.csit.fsu.edu/about.html) (8). An asterisk (*) beside a branch represents significant statistical support for the clade subtending that branch (p<0.001 in the zero-branch–length test) and bootstrap support >75%. Scale bar indicates nucleotide substitutions per site.