Analysis of the whole-genome sequence of an ASF virus (Asfarviridae: Asfivirus: African swine fever virus) isolated from a wild boar (Sus scrofa) at the border between Russian Federation and Mongolia

Abstract

Introduction. The causative agent of African swine fever (Asfarviridae: Asfivirus: African swine fever virus) (ASF) is a double-stranded DNA virus of 175–215 nm. To date, 24 of its genotypes are known. Clustering of ASF genotype II isolates is carried out by examining a limited number of selected genome markers. Despite the relatively high rate of mutations in the genome of this infectious agent compared to other DNA viruses, the number of known genome molecular markers for genotype II isolates is still insufficient for detailed subclustering. The aims of this work were the comparative analysis of ASFV/Zabaykali/WB-5314/2020 virus isolate and determination of additional molecular markers which can be used for clustering of viral genotype II sequences. Material and methods. ASF virus isolate ASFV/Zabaykali/WB-5314/2020 was used to extract genomic DNA (gDNA). Sequencing libraries were constructed using the Nextera XT DNA library prepare kit (Illumina, USA) using the methodology of the next generation sequencing (NGS). Results. The genome length was 189,380 bp, and the number of open reading frames (ORFs) was 189. In comparison with the genome of reference isolate Georgia 2007/1, 33 single nucleotide polymorphisms (SNPs) were identified, of which 13 were localized in the intergenic region, 10 resulted to the changes in the amino acid sequences of the encoded proteins, and 10 affected the ORF of ASF virus genes. Discussion. When analyzing intergenic regions, the ASFV/Zabaykali/WB-5314/2020 isolate is grouped separately from a number of isolates from Poland and three isolates from People’s Republic of China (PRC), since it does not harbor additional tandem repeat sequence (TRS). At the same time, the construction of a phylogenetic tree based on DP60R gene sequencing relates ASFV/Zabaykali/WB-5314/2020 to isolates from PRC and Poland. Moreover, phylogenetic analysis of full-genome sequences confirmed previous studies on the grouping of viruses of genotype II, and as for the studied isolate, it was grouped with the variants from China. Conclusion. A new variable region was identified, the DP60R gene, clustering for which gave a result similar to the analysis of full-length genomes. Probably, further study of the distribution of ASF virus isolates by groups based on the analysis of this gene sequences will reveal its significance for studying the evolution of the virus and its spread.

A Guide to Molecular Characterization of Genotype II African Swine Fever Virus: Essential and Alternative Genome Markers

“…This SNP was initially observed in the complete genome sequence of ASFV, isolated between 2016 and 2019 from Poland [ 40 ]. The identical substitution was verified for isolates from Ukraine, Moldova, European countries (Estonia, the Czech Republic, Belgium, Hungary, and Germany), all isolates sequenced from China, and the Far Eastern Federal District of Russia ( Figure 9 ) [ 14 , 43 , 44 , 45 , 46 ].…”

“…Both substitutions were non-synonymous and led to alterations in the predicted amino acid sequence (Asn 329 Ser in MGF-360-10L and Lys 323 Glu in MGF-505-9R ). These SNPs were detected in five ASFV isolates from the Far Eastern Federal District of Russia (ASFV/Primorsky/19/WB-6723 [MW306191], ASFV/Amur/19/WB-6905 [MW306190], ASFV/Zabaykali/2020/WB-5314 [MZ325862], and ASFV/Zabaykali/2020/DP-4905 OP510033]) [ 14 , 44 , 45 , 46 ].…”

Whole genome sequencing and phylogenetic analysis of African swine fever virus detected in a backyard pig in Mongolia, 2019

“…It has a high degree of nucleotide identity (>97%) with ASFVs recently detected in Eastern Europe and Asia (data not shown). It was found to cluster with the ASFV/Zabaykali/WB5314/2020|Russia|2020 virus, which was identified at the border between Russia and Mongolia in 2020 ( Figure 1 ) ( 5 ), suggesting that transboundary spread of ASF occurred through close geographic proximity. In late 2020, ASF-related mass mortality of wild boar was observed in MinJiin Khangai mountain, Mungunmorit soum of Tuv province, and Yeroo soum of Selenge province, which are remote areas of Mongolia bordering with Russia.…”

“…A total of 105 farms and holdings were affected by the disease, resulting in the death or elimination of more than 3,000 exposed pigs (> 10 % of the total pig population in Mongolia) ( 4 ). While complete genome sequences of ASFV have been reported from several countries affected by ASF ( 5 – 12 ), a complete genome sequence of ASFV from Mongolia has not been published. However, several characterizations of the ASFV strain from the 2019 outbreak in Bulgan province, Mongolia have been reported in a previous study: partial p72, full p54, partial pB602L, and partial CD2v genes, as well as a 356-bp fragment between the I73R and I329L genes ( 2 ).…”