Fig. 1

Schematic representation of target sequences along an HCMV genome. Shown is an overview of polymorphic amplified regions and their genetic diversity along the HCMV genome strain Merlin (AY446894). The figure consists of four separate tracks. In the top track, a mini-map of the genome with a total bases of 235,646 is shown. Annotated CDS and non-coding RNAs are depicted in grey and black, respectively. Target regions for amplicon generation are depicted in red and are described in detail in track 2–4. For track 2, defined polymorphic regions were put through a blastn search. Over 200 published haplotypes for the described regions were aligned. The mean pairwise identity over all pairs in the column is depicted. Green: 100% identity, greenish-brown: at least 30% identity but less than 100%, red: less than 30%. Displayed above the sequences (3rd track), grey and black arrows again represent CDS and non-coding RNAs, respectively. Forward and reverse primer (red and blue) are depicted below the sequence. The bottom track indicates individual fragment sizes and GC content of eight polymorphic target regions. Annotations were generated with geneious prime 2019.0.3