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

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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.

About the authors

A. Mazloum

FGBI «Federal Centre for Animal Health» («ARRIAH»)

Author for correspondence.
Email: ali.mazloum6@gmail.com
ORCID iD: 0000-0002-5982-8393

Ali Mazloum, Ph.D, Researcher, FGBI «ARRIAH» Federal State Budgetary Institution «Federal Center for Animal Health»

Vladimir region, Vladimir city, Yuryevets microdistrict, 600901

Russian Federation

A. S. Igolkin

FGBI «Federal Centre for Animal Health» («ARRIAH»)

Email: igolkin_as@arriah.ru
ORCID iD: 0000-0002-5438-8026

A.S. Igolkin, Ph.D, Head of reference laboratory for ASF, FGBI «ARRIAH» Federal State Budgetary Institution «Federal Center for Animal Health»,

Vladimir region, Vladimir city, Yuryevets microdistrict, 600901

Russian Federation

A. R. Shotin

FGBI «Federal Centre for Animal Health» («ARRIAH»)

Email: shotin@arriah.ru
ORCID iD: 0000-0001-9884-1841

A.R. Shotin, postgraduate student, leading veterinarian, FGBI «ARRIAH» Federal State Budgetary Institution «Federal Center for Animal Health»,

Vladimir region, Vladimir city, Yuryevets microdistrict, 600901

Russian Federation

N. G. Zinyakov

FGBI «Federal Centre for Animal Health» («ARRIAH»)

Email: zinyakov@arriah.ru
ORCID iD: 0000-0002-3015-5594

N.G. Zinyakov, Ph.D, Senior Researcher, FGBI «ARRIAH» Federal State Budgetary Institution «Federal Center for Animal Health»,

Vladimir region, Vladimir city, Yuryevets microdistrict, 600901, 

Russian Federation

N. N. Vlasova

FGBI «Federal Centre for Animal Health» («ARRIAH»)

Email: vlasova_nn@arriah.ru
ORCID iD: 0000-0001-8707-7710

N.N. Vlasova, doctor of sciences, Leading Researcher, FGBI «ARRIAH» Federal State Budgetary Institution «Federal Center for Animal Health»,

Vladimir region, Vladimir city, Yuryevets microdistrict, 600901

Russian Federation

E. V. Aronova

FGBI «Federal Centre for Animal Health» («ARRIAH»)

Email: aronova@arriah.ru
ORCID iD: 0000-0002-2072-6701

E.V. Aronova, Ph.D, Senior Researcher, FGBI «ARRIAH» Federal State Budgetary Institution «Federal Center for Animal Health»

Vladimir region, Vladimir city, Yuryevets microdistrict, 600901

Russian Federation

O. S. Puzankova

FGBI «Federal Centre for Animal Health» («ARRIAH»)

Email: puzankova@arriah.ru
ORCID iD: 0000-0003-1584-3169

O.S. Puzankova, Ph.D, Senior Researcher, FGBI «ARRIAH» Federal State Budgetary Institution «Federal Center for Animal Health»,

 

Russian Federation

V. L. Gavrilova

FGBI «Federal Centre for Animal Health» («ARRIAH»)

Email: gavrilova@arriah.ru
ORCID iD: 0000-0001-5843-2779

V.L. Gavrilova, Ph.D, Researcher, FGBI «ARRIAH» Federal State Budgetary Institution «Federal Center for Animal Health»

Vladimir region, Vladimir city, Yuryevets microdistrict, 600901

Russian Federation

I. V. Shevchenko

FGBI «Federal Centre for Animal Health» («ARRIAH»)

Email: shevchenko@arriah.ru
ORCID iD: 0000-0001-6482-7814

I.V. Shevchenko, Ph.D, Senior Researcher, FGBI «ARRIAH» Federal State Budgetary Institution «Federal Center for Animal Health»

Vladimir region, Vladimir city, Yuryevets microdistrict, 600901

Russian Federation

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Copyright (c) 2022 Mazloum A., Igolkin A.S., Shotin A.R., Zinyakov N.G., Vlasova N.N., Aronova E.V., Puzankova O.S., Gavrilova V.L., Shevchenko I.V.

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