Natural viral bloom is polyclonal.

<p>Sequence variation within a gene of the blooming AMDV3b viral population (345 bp field of view). The top bar of the figure represents an 18 kb contig sequence of AMDV3b, with predicted genes shown as boxes. Below the contig, is a close-up view of sequence variation within a single gene. White bars represent aligned sequencing reads, while colored bars indicate SNPs relative to the composite sequence. The black region is a large deleted sequence block in one individual viral genome. Distinct viral sub-populations are captured during the bloom, each sharing common SNPs. Also shown in the figure are regions of the AMDV3b contig that match G-plasma spacers: closed circles in the contig represent perfect matches and open circles represent imperfect matches. When the match between G-plasma spacer and AMDV3b protospacer occurs within a predicted gene, the circle is placed inside the corresponding gene box; matches to intergenic regions are shown below on the contig line.