FIG. 3.

Alignments of primers and probes with consensus sequences of BKV subtypes. Sequences corresponding to forward primers (left), probes (center), and reverse primers (right) are shown for each primer/probe set, along with corresponding regions of consensus sequences representing BKV subtypes Ia, Ic, III, IV, V, and VI. V3a and T3a indicate sequences of the modified primers and probes derived from the V3 and T3 sequences, respectively, used in the V3T3 assay. The numbers indicate positions in the BKV genome based on the Dunlop reference strain (GenBank accession no. V01108). Subtypes with consensus sequences identical to those of a given primer/probe set are omitted. Nucleotides identical to the primer sequence at each position are shown as periods. IUPAC ambiguity codes are used where the consensus sequence could not be defined as a simple majority of sequences in a subtype. The codes used are defined as follows: S, G/C; Y, C/T; W, A/T. The position in the V2 probe appearing below the asterisk is occupied by a modified base (Nanogen, Inc., personal communication). Sequences of all reverse primers and T1, V2, and T2 probes are shown as the reverse complements of the synthesized oligonucleotides.