Recombination drives the emergence of orf virus diversity: evidence from the first complete genome sequence of an Indian orf virus isolate and comparative genomic analysis

Abstract

Contagious pustular dermatitis is a disease that primarily infects small ruminants and possesses zoonotic potential. It is caused by orf virus (ORFV), a member of the genus Parapoxvirus. In this study, we evaluated an ORFV outbreak in goats in Madhya Pradesh, a state in central India, during 2017. The transboundary potential of this virus was evaluated by constructing phylogenetic trees. The complete genome sequence of an ORFV isolate named Ind/MP/17 was found to be 139,807 bp in length with 63.7% GC content and 132 open reading frames (ORFs) flanked by 3,910-bp inverted terminal repeats (ITRs). An investigation into evolutionary parameters such as selection pressure (θ = dN/dS) and nucleotide diversity (π) demonstrated that ORFV has undergone purifying selection. A total of 40 recombination events were identified, 21 of which were evident in the Ind/MP/17 genome, indicating its ability to generate new variants.

Fig. 1

Phylogenetic analysis based on ORFV011 sequences of ORFV. The phylogenetic tree was constructed by the maximum-likelihood method with the GTR model, using MEGA 6.0 software. The numbers at the branching points indicate the bootstrap support calculated for 1,000 replicates. The black triangle indicates the isolate from the present study.

Fig. 2

Analysis of the ITRs of ORFV. (A) Left end (5’) sequence alignment of 14 complete ORFV genome sequences, showing a terminal BamHI site (green box) and telomere resolution motifs (red box) (ATTTTTT-N(8)-TAAAT). (B) Right end (3’) sequence alignment of 14 complete ORFV genome sequences, showing a terminal BamHI site (green box) and telomere resolution motifs (red box) (ATTTTTT-N(8)-TAAAT).

Fig. 3

Phylogenetic analysis of PPVs. Nineteen complete genome sequences, including the terminal repeats, were aligned to construct a phylogenetic tree with 1000 bootstrap replicates using the maximum-likelihood method with the GTR model. The black triangle indicates the ORFV isolate from the present investigation.