Figure 1.

Representative recombinant sequences identified by bootscans implemented in Simplot. Scans were generated using a sliding window of 140 nucleotides, moving 10 nucleotides at a time. The x-axis shows nucleotide positions on the VP-1 gene sequence (Dun numbering). The y-axis depicts the percent agreement in the permuted trees. The query sequences are indicated in the title line starting with patient number followed by clone number. Thus, 20CL7 refers to clone #7 from patient #20. Accession numbers of published sequences used in this plot are: Dunlop (V01108), TW-3 (AB211391), and ETH-3 (AB263916).

Figure 1A illustrates a recombinant sequence that conforms to type I in the initial segment (blue line) and type IV in the final segment (red line). A type II outgroup sequence (II_ETH, green line) was used to generate the plot.

Figure 1B depicts a more complex recombinant sequence with an initial segment conforming to genotype IV (blue line), which is followed by a short genotype II sequence (red line), following which the sequence reverts to genotype IV (blue line). BKV strain Dun (Type I) was used as the outgroup sequence (green line).