Molecular Characterization of African Swine Fever Virus Isolates in Estonia in 2014-2019.

Annika Vilem,Imbi Nurmoja,Raquel Nieto,Arvo Viltrop,Tarmo Niine,Carmina Gallardo,Taavi Riit

doi:10.3390/pathogens9070582

Abstract

After the extensive spread of the African swine fever virus (ASFV) genotype II in Eastern Europe, the first case of African swine fever (ASF) in Estonia was diagnosed in September 2014. By the end of 2019, 3971 ASFV-positive wild boars were found, and 27 domestic pig outbreaks were reported. A selection of ASFV isolates from wild boar and domestic pigs (during the period of September 2014–2019) was molecularly characterized using standardized genotyping procedures. One of the proven markers to characterize this virus is the central variable region (CVR) within the B602L gene. In summer 2015, a new ASFV genotype II CVR variant 2 (GII-CVR2) was confirmed in Estonia. The results suggest that the GII-CVR2 variant was only confirmed in wild boar from a limited area in southern Estonia in 2015 and 2016. In addition to GII-CVR2, a single nucleotide polymorphism (SNP) that resulted in amino acid change was identified within the genotype II CVR variant 1 (GII-CVR1). The GII-CVR1/SNP1 strain was isolated in Estonia in November 2016. Additional GII-CVR1/SNP1 cases were confirmed in two neighbouring counties, as well as in one outbreak farm in June 2017. Based on the available data, no GII-CVR2 and GII-CVR1/SNP1 have been reported by other affected European countries. The spread of variant strains in Estonia has been limited over time, and restricted to a relatively small area.

Highlights

African swine fever (ASF) is a viral disease of swine that can lead to high mortality in domestic pigs and wild boar (Sus scrofa) while being asymptomatic in wild suid reservoir hosts in Africa [1].ASF causes important economic damage due to mortality and production losses
Further and amino acid sequence analyses revealed three different variants co-circulating in the country, two of them within the African swine fever virus (ASFV) GII-CVR1, according to the nomenclature of amplicon of 400 bp were 100% homologous to the reference sequence of Georgia 2007/1
Most published studies use the molecular characterization of vp72 or/and variable regions containing an array of the tandem repeat sequences (TRS) for genotyping and subgrouping closely related isolates [16,17,21,26,29,44]

Summary

Introduction

ASF causes important economic damage due to mortality and production losses. The length of the African swine fever virus (ASFV) genome can vary remarkably from 170 to 194 kbp, and the number of genes can vary from 150 to 167, depending on the isolate [4,5,6,7]. The gain or loss of ORFs from the multigene families (MGF) encoded by the virus is the primary reason behind the differences in the virus’s genome length and gene number [5,6,9]. A large number of highly variable multigene families in the genome of ASFV is one of the biggest challenges for understanding the functionality of the virus [5]

Methods

Results

Conclusion