Additional file 2 of New approach for genomic characterisation of equine sarcoid-derived BPV-1/-2 using nanopore-based sequencing

Additional file 2. Overview of all used primer sets for the amplification of complete BPV genomes. The primer set used in batch 1 (V1) consisted of ten overlapping amplicons, divided across two pools, that spanned the complete BPV genome. These primers were degenerated at multiple positions to allow them to amplify nearly all members of the species Deltapapillomavirus 4, including types 1, 2 and 13. To increase target-specificity, reducing the fraction of non-usable data and allowing more samples to be run on the same flow cell, a second version of the primer set was designed (V2). The number of amplicons in this second set was reduced to eight and their specificity was limited to BPV-1 and BPV-2, allowing the degree of degeneracy to be lowered considerably. Because two of the genomes from batch 2 contained a large deletion, disrupting one of the primer sites and leading to amplicon dropout, an alternative primer was designed for one of the amplicons. This slightly modified primer set (V3) was used to amplify a final batch of 30 samples.