Genomic characterization of a novel Epsilonpapillomavirus associated with pigmented papillomas in a red deer (Cervus elaphus)

Two of a group of 15 farmed European red (Cervus elaphus elaphus) X wapiti (C. e. canadensis) deer stags developed multiple persistent pigmented squamous papillomas (warts) on their chins. DNA was extracted from a papilloma and a short section of DNA from a novel papillomavirus (PV) was amplified. This short sequence was used to design 'outward facing' primers to amplify the remainder of the circular PV DNA. The PCR product was sequenced using next-generation sequencing and the full genome of the PV, consisting of 8082 bp, was assembled and analysed. The novel PV was designated Cervus elaphus papillomavirus (CePV) type 2. The putative coding regions of CePV2 were predicted to produce four early and two late proteins with two other potential ORFs also noted. Phylogenetic analysis of ORF L1 revealed greater than 60 %, but less than 70 % similarity, to Bos taurus papillomavirus (BPV) types -5 and -7. As both BPV5 and BPV7 are Epsilonpapillomavirus 1, CePV2 is proposed as the first Epsilonpapillomavirus 2 PV type. This is the first EpsilonPV to be identified in a non-bovine species and the first non-DeltaPV to be identified as a cause of disease in any deer species.