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. 2024 Dec 11;16(12):1907.
doi: 10.3390/v16121907.

Unique Nucleotide Polymorphism of African Swine Fever Virus Circulating in East Asia and Central Russia

Roman Chernyshev  1 , Ali Mazloum  2 , Nikolay Zinyakov  1 , Ivan Kolbin  1 , Andrey Shotin  1 , Fedor I Korennoy  1 , Alexander V Sprygin  1 , Ilya A Chvala  1 , Alexey Igolkin  1
Affiliations

Unique Nucleotide Polymorphism of African Swine Fever Virus Circulating in East Asia and Central Russia

Roman Chernyshev et al. Viruses. .

Abstract

The lack of data on the whole-genome analysis of genotype II African swine fever virus (ASFV) isolates significantly hinders our understanding of its molecular evolution, and as a result, the range of single nucleotide polymorphisms (SNPs) necessary to describe a more accurate and complete scheme of its circulation. In this regard, this study aimed to identify unique SNPs, conduct phylogenetic analysis, and determine the level of homology of isolates obtained in the period from 2019 to 2022 in the central and eastern regions of Russia. Twenty-one whole-genome sequences of genotype II ASFV isolates were assembled, analyzed, and submitted to GenBank. The isolates in eastern Russia form two clades, "Amur 2022" and "Asia". Within the latter clade, five subclusters can be distinguished, each characterized by a unique set of SNPs and indels. The isolates from the central regions of Russia (2019; 2021) form the "Center of Russia" clade, with two subclusters, "Bryansk 2021" and "Center of Russia 2021" (bootstrap confidence index = 99). The presence of the previously unique genetic variant ASFV for the Kaliningrad region in the wild boar population of the Khabarovsk region (eastern Russia; 2021) has also been confirmed.

Keywords: African swine fever virus; Asia; genotype II; molecular epidemiology; single nucleotide polymorphisms.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Epidemic situation on ASF in the Russian Federation from 2019 to 2022. The isolates covered by this study are indicated in large print.
Figure 2
Figure 2
The ratio of absorbance at A260/A230 (low molecular weight purification rate, reference ≥ 2.0) (A), number of reads (B), A260/A280 (protein purification rate, reference ≥ 1.8) wavelengths for gDNA samples (C), number of ASFV specific reads (D), and mean coverage (E).
Figure 2
Figure 2
The ratio of absorbance at A260/A230 (low molecular weight purification rate, reference ≥ 2.0) (A), number of reads (B), A260/A280 (protein purification rate, reference ≥ 1.8) wavelengths for gDNA samples (C), number of ASFV specific reads (D), and mean coverage (E).
Figure 3
Figure 3
Percent of identity between the studied isolates and ASFV reference strains characterized in geographically separated areas of Eurasia.
Figure 4
Figure 4
Phylogram showing relatedness between the twenty-one isolates from this study and the most well-known ASFV reference strains from Genbank. Note: the isolates covered by this research are labeled with •.
Figure 5
Figure 5
Maximum likelihood phylogenetic tree indicating the relationship of ASFV genotype II sequences, using selected ORFs MGF 110-1L (A), MGF 505-9R (B), NP419L, (C) and I267L (D). Note: the isolates covered in this study are labeled with a black dot; the original (root) and Genetic variant (I) are marked with blue while Genetic variant (II) is green.
Figure 6
Figure 6
(A) Nucleotide sequence alignment of the intergenic region B602L/B385R of ASFV genotype II isolates, showing the formation of two variants. (B) Maximum likelihood phylogenetic tree of showing the relation between ASFV isolates based on the analysis of MGF 360-10L. Variant II is indicated in green; other isolates belong to cluster Asia (blue). Isolates from this study are labeled with a black dot.
Figure 7
Figure 7
Alignment of IGR I73R/I329L sequences after genome assembly (A) and after Sanger sequencing (B). Note: The blue color indicates the IGR-I variant; the green color indicates IGR-II; the isolates covered in this study are labeled black background color.
Figure 8
Figure 8
The molecular and epidemiological pattern of ASFV genotype II circulation in Europe and Asia, based on whole genome analysis of isolates.
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