African swine fever virus () strains from the central regions of Russia, carrying variant 5 of the central variable region (CVR), are characterized by tandem duplication in the intergenic region.

Abstract

INTRODUCTION: The high economic losses and the lack of effective and safe vaccines against African swine fever (ASF) indicate the need for further in-depth studies of the virus genome, its changes and the circulation of genetic lineages. Whole genome sequencing of virus isolates is best suited for this purpose. THE AIM OF THE STUDY: Whole-genome analysis of African swine fever virus (ASFV) isolates obtained in the Lipetsk, Penza and Tambov regions in 2016-2021 and identification of additional diversity markers within the genetic lineage. MATERIALS AND METHODS: Domestic pig tissue samples were analyzed using whole-genome sequencing and Sanger sequencing. The following programs were used for sequence assembly: CLC Genomics Workbench 22, Trimmomatic v. 0.39, SPAdes v. 4.2.0, BWA-MEM v. 0.7.17-r1188 and bcftools v.1. 22. The phylogenetic tree was constructed in MEGA11 based on the alignment in MAFFT v. 7.526 with 67 genomes from GenBank. RESULTS: Based on the presence of MGF 360-10L III polymorphism, the analyzed isolates belong to the CVR-V variant of the Russia genetic lineage of the Georgia 2007 clade. Based on the order of formation of MGF 360-10L III and CVR-V, any sequences carrying CVR-V belong to the same genetic lineage. A 12-nucleotide insertion CAGTCTATAAGA was detected, forming a tandem duplication in, and polymorphisms inand in genesandwere proposed as having phylogenetic potential for differentiation ASFV strains in the central regions of Russia. CONCLUSION: The proposed new potential diversity markers have a resolving power for ASFV strains from Central Russia.