Whole genome sequencing and phylogenetic analysis of a sheeppox virus isolate obtained during the 2023 outbreak in Aktobe, Kazakhstan

Authors: Urzhan Omarbekova, Matenova Nazerke, Andrey Bogoyavlenskiy, Yergali Moldakhanov, Madina Alexyuk, and Aidar Mukhametkaliyev

Ger. J. Vet. Res 2025. vol. 5, Iss. 4 pp:135-143
Doi: https://doi.org/10.51585/gjvr.2025.4.0170

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Abstract:

Sheeppox (SPPV) is a contagious viral disease affecting sheep and characterized by fever and skin lesions. SPPV re-emerged in Kazakhstan in 2023, with outbreaks recorded in the East Kazakhstan and Aktobe regions, including the first case in Katon-Karagay in 50 years. Affected sheep exhibited typical clinical signs of sheeppox, prompting laboratory confirmation and genomic investigation. This study aimed to characterize the circulating virus genome while assessing its relationship to global strains. Viral DNA extracted from skin lesions was sequenced on the Illumina MiSeq Platform, and the genome was assembled and analyzed using standard bioinformatics tools. Phylogenetic comparisons were performed against 27 complete sheeppox virus genomes from GenBank. The resulting genome, deposited under accession number PQ014465, measured 149,830 bp with 147 predicted ORFs and 25% GC content. Phylogenetic analysis showed that the Kazakhstan isolate (PQ014465) was closely related to strains circulating in Kazakhstan and European Russia, with an identity of 99,89%. A total of 24 nucleotide substitutions in several genes, and a major deletion (134 bp) in gene 117 were identified in the isolate PQ014465. Additionally, this isolate exhibited five unique amino acid substitutions in genes 8 (I74→L; S233→T), 118 (K73→R), and 134 (L608→F; N844→D). These findings provide the first genomic characterization of the 2023 outbreaks, reveal the unique molecular profile of the regional lineage, and underscore the need for sustained genomic surveillance to guide effective control strategies. The data obtained will be of significant interest to national and regional veterinary authorities.

Keywords:

Deduced amino acids, Evolutionary relationships, Genomic sequence, Nucleotide substitutions, Phylogenetic tree, Poxviridae, Variola ovina

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