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.