Federal Centre for Animal Health (ARRIAH).
Vopr Virusol. 2024 Nov 9;69(5):481-494. doi: 10.36233/0507-4088-263.
The lack of data on the whole-genome sequences of African swine fever virus (ASFV) variants circulating on the territory of the left bank of the Dnieper River complicates the understanding of the molecular evolution of the virus and the character of the epidemic process development in Russia and Ukraine. Understanding the genetic divergence and phylogenetic relatedness of isolates can largely adjust the strategy of general and specific prevention of the disease. The aim of the study - search and description of unique mutations (deletions/insertions/substitutions) in isolates collected from domestic pigs in Donetsk, Luhansk and Zaporozhye regions in 2023; determination of relatedness and level of homology with reference strains of ASFV genotype II; sub-genotyping and clustering of isolates based on whole-genome analysis.
The samples used were a culture suspension of porcine bone marrow (PBM) cells containing ASFV isolates obtained from pathologic material from domestic pig carcasses. Genomic DNA was prepared by purification and concentration of virus followed by phenol-chloroform extraction of total nucleic acid. The high-throughput sequencing process was performed using MGI technology. Consensus sequences were assembled by mapping reads to the reference genome of strain Georgia 2007/1.
All isolates are assigned to genotype II, have a monophyletic origin, are phylogenetically close to the clusters «Europe» (4/5) and «Bryansk 2021» (1/5), and are divergent from the original parental genetic variants that make up the enlarged clades. In addition, numerous substitutions in the loci of the multigene family , , and , encoding virulence proteins, were detected in 4 isolates from Donetsk and Zaporozhye regions.
The phylogeny of the genotype II ASFV, which originated from the reference strain Georgia 2007/1, is shown to be sufficient for isolate differentiation. The presented data are of theoretical and practical importance for domestic and international ASFV surveillance.
由于缺乏关于在第聂伯河左岸流行的非洲猪瘟病毒 (ASFV) 变体的全基因组序列数据，这使得我们难以理解该病毒的分子进化以及俄罗斯和乌克兰疫情发展的特点。了解分离株的遗传差异和系统发育关系，在很大程度上可以调整疾病的一般和具体预防策略。本研究的目的是：搜索并描述 2023 年在顿涅茨克、卢甘斯克和扎波罗热地区从家猪中采集的分离株中的独特突变（缺失/插入/替换）；确定与 ASFV 基因型 II 的参考株的亲缘关系和同源性水平；基于全基因组分析对分离株进行亚基因分型和聚类。
所用样本为来自家猪尸体病理材料的含有 ASFV 分离株的猪骨髓（PBM）细胞培养悬浮液。基因组 DNA 通过病毒的纯化和浓缩以及总核酸的酚-氯仿抽提来制备。高通量测序过程使用 MGI 技术进行。将读序列映射到参考基因组菌株 Georgia 2007/1 上，以组装一致序列。
所有分离株均被归为基因型 II，具有单系起源，在系统发育上与“欧洲”（4/5）和“Bryansk 2021”（1/5）聚类密切相关，与构成扩大进化枝的原始亲本遗传变体存在分歧。此外，在来自顿涅茨克和扎波罗热地区的 4 个分离株中，还检测到多基因家族、、和编码毒力蛋白的基因座中存在大量的替换。
起源于参考菌株 Georgia 2007/1 的基因型 II ASFV 的系统发育足以用于分离株的分化。所提供的数据对于国内外的 ASFV 监测具有理论和实际重要性。
