Isolation and whole-genome characterization of an Orf virus strain from a goat in Binzhou, Shandong Province, China

Abstract

Orf virus (ORFV), a member of the genus Parapoxvirus within the family Poxviridae, causes contagious ecthyma in sheep and goats and is zoonotic. In this study, a scab sample collected from an affected goat in Binzhou, Shandong Province, China, was subjected to virus isolation and whole-genome characterization. ORFV was isolated in HeLa cells, and its identity was confirmed by F1L-targeted PCR with Sanger sequencing and indirect immunofluorescence assays using anti-F1L and anti-B2L polyclonal antibodies. Reference-independent de novo assembly of Illumina reads generated a 133,972-bp near-complete genome with a GC content of 64.05%, containing 122 predicted coding sequences and one tRNA. Terminal hairpin structures and complete inverted terminal repeats were not fully resolved. ORF-YW01 showed the highest average nucleotide identity with strain SY17 (MG712417.1; 98.82%), whereas the highest alignment percentage was observed with strain 28BD (PX497028.1; 98.58%). Phylogenetic analysis also placed ORF-YW01 in a sister relationship with strain 28BD. RDP5 analysis identified three potential recombination signals; however, breakpoint and parental assignments remained uncertain, and BootScan analysis did not show a consistent parental-switching pattern. These signals were therefore not considered confirmed recombination events. This study provides a near-complete genomic record of an ORFV field isolate from Binzhou and establishes a genome-scale reference for future surveillance and direct comparison of ORFV isolates from Shandong Province.