Recombination may drive the emergence of Orf virus diversity: Evidence from the first complete genome of Indian Orf virus and comparative genomic analysis.

Abstract

Contagious ecthyma is a zoonotic disease caused by the Parapoxvirus virus, Orf (ORFV) affecting sheep, goats, humans and is widely distributed across the world, including India. Here, we have investigated the 2017 ORFV outbreak in goats that occurred in the central Indian state of Madhya Pradesh. The outbreak was characterized by a moderate rate of morbidity (up to 20%) with no mortality. Phylogenetic analysis of four partial genes, such as ORFV011, ORFV020, ORFV059, and ORFV108, revealed the transboundary potential of the virus by showing its relationship with a distinct geographical area. We characterized the complete genome of this strain named Ind/MP and performed comparative genomic analysis. The Ind/MP whole genome consists of 139,807 bp with GC content 63.7%. The genome contains 132 potential open reading frames (ORFs) flanked by inverted terminal repeats (ITRs) of 3,910 bp at both ends having terminal BamHI sites and conserved telomere resolution sequences. Population genetic parameters such as nucleotide diversity (π), selection pressure analysis (θ=dN/dS), etc. suggest that the ORFV resides under purifying selection. The potent molecular markers, such as Simple Sequence Repeats (SSRs) and compound SSRs (cSSRs) were more prevalent within the functional protein with the value 70% and 67%, respectively. A total number of forty recombination events were identified, out of which Ind/MP strain actively participate in twenty-one events suggesting that this strain can recombine for the generation of new variants.