Genomic and phylogenetic characterization of ChPV2, a novel goat PV closely related to the Xi-PV1 species infecting bovines

Anouk Willemsen,Firat Dogan,Alexander Van Den Boom,Eric Ehrke-Schulz,Julienne Dietz,Seval Bilge Dagalp,Anja Ehrhardt,Ignacio G Bravo

doi:10.1186/s12985-020-01440-9

Abstract

BackgroundPapillomaviruses (PVs) infecting artiodactyls are very diverse, and only second in number to PVs infecting primates. PVs associated to lesions in economically important ruminant species have been isolated from cattle and sheep.MethodsPotential PV DNA from teat lesions of a Damascus goat was isolated, cloned and sequenced. The PV genome was analyzed using bioinformatics approaches to detect open reading frames and to predict potential features of encoded proteins as well as putative regulatory elements. Sequence comparison and phylogenetic analyses using the concatenated E1E2L2L1 nucleotide and amino acid alignments was used to reveal the relationship of the new PV to the known PV diversity and its closest relevants.ResultsWe isolated and characterized the full-genome of novel Capra hircus papillomavirus. We identified the E6, E7, E1, E2, L2, L1 open reading frames with protein coding potential and putative active elements in the ChPV2 proteins and putative regulatory genome elements. Sequence similarities of L1 and phylogenetic analyses using concatenated E1E2L2L1 nucleotide and amino acid alignments suggest the classification as a new PV type designated ChPV2 with a phylogenetic position within the XiPV genus, basal to the XiPV1 species. ChPV2 is not closely related to ChPV1, the other known goat PV isolated from healthy skin, although both of them belong confidently into a clade composed of PVs infecting cervids and bovids. Interestingly, ChPV2 contains an E6 open reading frame whereas all closely related PVs do notConclusionChPV2 is a novel goat PV closely related to the Xi-PV1 species infecting bovines. Phylogenetic relationships and genome architecture of ChPV2 and closely related PV types suggest at least two independent E6 losses within the XiPV clade.

Highlights

Papillomaviruses (PVs) infecting artiodactyls are very diverse, and only second in number to PVs infect‐ ing primates
Even though most PV types share less than 60% of L1 nucleotide identity with PVs from other genera, their assignment to species and genera requires the analysis of phylogenetic position, genome organization, biology and pathophysiology[9]
PVs infecting ruminants belong within the Delta, Xi, Epsilon, Dyoxi, Dyokappa, Phiand DyolambdaPV genera within the Beta-XiPV and Delta-ZetaPV crown groups. In this manuscript we have focused on the description of a novel PV, Capra hircus papillomavirus 2 (ChPV2), previously identified in teatpapillomas of a Damascus goat in Turkey [12]

Summary

Introduction

Papillomaviruses (PVs) infecting artiodactyls are very diverse, and only second in number to PVs infect‐ ing primates. Papillomaviruses (PVs) are small epitheliotropic viruses infecting mammals, reptiles, birds and fish. They are found in healthy skin and mucosa [1], benign proliferative epithelial lesions, and malignant cancers [2,3,4]. SaPV1 is very divergent from other PVs, and has a unique genome organization containing only the URR, E1, E2, L2, and L1 genes [10], shared by other PVs genomes isolated from other fish species (GenBank accessions MH510267, MH616908, MH617143, and MH617579). The Secondpapillomavirinae consist of 52 genera named after the Greek alphabet and variations thereof Within this clade, genera can be grouped into crown-groups: four well-defined clades spanning AlphaOmikronPVs, Beta-XiPVs, Lambda-MuPVs, DeltaZetaPVs, an additional, ill-defined clade of PVs infecting other mammals, and a yet unclassified clade, consisting of PVs infecting birds and turtles [6]

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Conclusion