Genetic Characterization of the Central Variable Region in African Swine Fever Virus Isolates in the Russian Federation from 2013 to 2017

Abstract

African swine fever virus (ASFV), classified as genotype II, was introduced into Georgia in 2007, and from there, it spread quickly and extensively across the Caucasus to Russia, Europe and Asia. The molecular epidemiology and evolution of these isolates are predominantly investigated by means of phylogenetic analysis based on complete genome sequences. Since this is a costly and time-consuming endeavor, short genomic regions containing informative polymorphisms are pursued and utilized instead. In this study, sequences of the central variable region (CVR) located within the B602L gene were determined for 55 ASFV isolates submitted from 526 active African swine fever (ASF) outbreaks occurring in 23 different regions across the Russian Federation (RF) between 2013 and 2017. The new sequences were compared to previously published data available from Genbank, representing isolates from Europe and Asia. The sequences clustered into six distinct groups. Isolates from Estonia clustered into groups 3 and 4, whilst sequences from the RF were divided into the remaining four groups. Two of these groups (5 and 6) exclusively contained isolates from the RF, while group 2 included isolates from Russia as well as Chechnya, Georgia, Armenia, Azerbaijan and Ukraine. In contrast, group 1 was the largest, containing sequences from the RF, Europe and Asia, and was represented by the sequence from the first isolate in Georgia in 2007. Based on these results, it is recommended that the CVR sequences contain significant informative polymorphisms to be used as a marker for investigating the epidemiology and spread of genotype II ASFVs circulating in the RF, Europe and Asia.

A multi gene-approach genotyping method identifies 24 genetic clusters within the genotype II-European African swine fever viruses circulating from 2007 to 2022

“…Even though the resolving power of this gene region in isolates from Africa ( 28 – 34 ) and the polymorphisms observed in isolates from Estonia ( 14 ), only two SNP-based CVR variants were detected in this study in wild boar viruses from Poland (CVR1-SNP2) and Lithuania (CVR1-SNP3). Recent studies describe the presence of additional CVR variants in isolates from Russia ( 35 ) and China ( 19 ) based on the presence of SNPs. However, the variants described in this study were unique and were not further identified in any of the ASFVs sequenced or available in the GenBank.…”

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

“…The spread of ASFV across Europe and into Asia has been rapid, vast, and in the face of no effective vaccine, it will probably keep expanding its range into new countries globally [ 48 ]. While spreading across Eurasia, the clonal populations of the virus accrue mutations that can be common in a region and used for evaluating ASFV radiation events [ 24 , 30 , 41 ]. In this regard NGS promotes the generation of complete genome sequences and can be employed to track the virus from one outbreak to another, identifying innovative variants and assigning sequences to a specific variant group [ 14 , 26 , 37 ].…”

“…These SNPs were synonymous (C/T) at position 480 and A/G at position 616. The latter SNP resulted in a threonine (T) exchange of alanine (A) at position 206 of the complete B602L predicted protein [ 24 ]. An alignment of the partial CVR ( B602L ) nucleotide sequence of different isolates indicating each of the six groups is depicted in Figure 2 .…”

Differentiation of African Swine Fever Virus Strains Isolated in Estonia by Multiple Genetic Markers

“…The K145R, O174L, and MGF505-5R sequence analyses were performed in comparison with the Georgia 2007/1 reference sequence (GenBank accession number FR682468.2) [ 13 ]. For the B602L gene-sequence alignment, the representatives of the previously detected Estonian CVR variant strains (GenBank accession numbers MT647548 and MT647527) [ 7 ], Lithuanian LT14/1490 (GenBank accession number KJ627204) [ 2 ], and Russian CVR variant strains (GenBank accession numbers ON098036, ON098025, ON098023 and ON098019) [ 19 ] were added. For IGR I73R/I329L analysis, the index case of ASFV in the EU was included (GenBank accession MK628478) [ 20 ] to sequence alignment.…”