First Record of Whole-Genome Sequencing of Cowpox Virus in Cattle and Water Buffaloes in Iraq: Genomic Characterization and Epidemiological Investigation
Abstract
Background: Cowpox virus (CPXV) is a zoonotic Orthopoxvirus of veterinary and public health importance, especially in livestock systems where pox-like cutaneous disease can impact animal welfare, milk production and occupational exposure. Genomic information on livestockassociated CPXV in Iraq remains limited. Materials and Methods: This study investigated CPXV in clinically affected cattle and water buffaloes with pox-like skin lesions in Basra Governorate, southern Iraq, using molecular detection, whole-genome sequencing, and phylogenomic analysis. Lesion-derived specimens, including swabs, crusts, scabs, and epithelial scrapings, were screened for Orthopoxvirus DNA, and selected positive samples with adequate DNA quality were subjected to whole-genome sequencing. Results: A total of 20 lesion-derived clinical samples were collected, comprising 13 samples from water buffaloes and 7 from cattle; 12 of 20 samples (60.0%) tested positive for Orthopoxvirus DNA by real-time PCR. Four complete CPXV genomes were generated: two cattle-derived isolates (LC895885.1 and LC909709.1) and two water buffalo-derived isolates (LC909707.1 and LC909708.1). Each genome comprised 224,499 bp and was deposited in the NCBI GenBank database. Pairwise whole-genome comparison showed 99.9996% nucleotide identity between the two buffaloderived isolates and 99.9844% between the two cattle-derived isolates; cattle-buffalo comparisons ranged from 99.9483% to 99.9644%. Maximum-likelihood phylogenetic analysis placed the four Iraqi genomes within the Cowpox virus group, with the Iraqi isolates forming a closely related local cluster near established CPXV reference genomes. Conclusions: These findings highlight the utility of lesion-derived specimens and genome-scale analysis for differentiating clinically similar pox-like diseases and for resolving the genomic relationships of livestockassociated Orthopoxviruses. To our knowledge, this study provides the first whole-genome characterization of CPXV detected in cattle and water buffaloes in Iraq and establishes baseline genomic data for future veterinary, regional genomic, and One Health surveillance efforts.