In this master's thesis, we designed a technique for reliably amplifying molluscum contagiosum virus (MOCV) whole genomes directly from clinical samples, in which the amount of viral DNA can vary. We first created a set of 59 oligonucleotide primers based on 64 publicly accessible MOCV genomes. We used both amplicon-based sequencing and total nucleic acid sequencing to test the approach on eight clinical samples (four MOCV1 and four MOCV2). All MOCV1 samples had full genome coverage during the initial experimentation phase, whereas MOCV2 samples only had partial genome coverage. We added 9 more primer pairs and carried out the sequencing again. This time, we covered the MOCV1 (98.4 %) and MOCV2 (97.0 %) genomes nearly completely. We discovered that numerous primers developed exclusively for MOCV1 functioned well on MOCV2, even when there were mismatches, as long as they weren't consecutive. We verified that the data from whole-genome sequencing was similar to our amplicon-based results. Lastly, we performed a theoretical coverage study for MOCV genomes. We discovered that our primers could cover more than 98 % of MOCV with up to two or three mismatches permitted. This approach proved to be a straightforward and cost-effective way of studying MOCV at the genomic level. It promises to be a very helpful technique for upcoming research on its evolution and future treatments.
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