Deletion at the 5’-end of Estonian ASFV strains associated with an attenuated phenotype

Abstract

African swine fever (ASF) was introduced into the Eastern European Union in 2014 and led to considerable mortality among wild boar. In contrast, unexpected high antibody prevalence was reported in hunted wild boar in north-eastern Estonia. One of the causative virus strains was recently characterized. While it still showed rather high virulence in the majority of experimentally infected animals, one animal survived and recovered completely. Here, we report on the follow-up characterization of the isolate obtained from the survivor in the acute phase of infection. As a first step, three in vivo experiments were performed with different types of pigs: twelve minipigs (trial A), five domestic pigs (trial B), and five wild boar (trial C) were inoculated. 75% of the minipigs and all domestic pigs recovered after an acute course of disease. However, all wild boar succumbed to infection within 17 days. Representative samples were sequenced using NGS-technologies, and whole-genomes were compared to ASFV “Georgia 2007/1”. The alignments indicated a deletion of 14560 base pairs at the 5’ end, and genome reorganization by duplication. The characteristic deletion was confirmed in all trial samples and local field samples. In conclusion, an ASFV variant was found in Estonia that showed reduced virulence.

Attenuated and non‐haemadsorbing (non‐HAD) genotypeIIAfrican swine fever virus (ASFV) isolated in Europe, Latvia 2017

“…The ASFV strains responsible of the European and China outbreaks have been classified as genotype II viruses and mostly induce an acute clinical form of the disease with mortality close to 100% Ge et al, 2018;Guinat et al, 2016). However, the increased seroprevalence found in certain areas of the affected EU countries over time, in addition to the recent description of ASFVs of moderated virulence suggest virus evolution towards less virulent forms Zani et al, 2018). Although most of the ASFV isolates cause haemadsorption (HAD) of erythrocytes to infected cells, there are several isolates that do not and these are referred to as non-haemadsorbing (non-HAD) isolates.…”

Genome comparison of African swine fever virus China/2018/Anhui XCGQ strain and related European p72 Genotype II strains

“…Most of the variation among ASFV genomes results from the gain and loss of the MGF members (Dixon, Chapman, Netherton, & Upton, 2013). Genome sequences of four genotype II strains have been reported (Chapman et al, 2011;Olesen et al, 2018;Zani et al, 2018). Among these strains, Estonia 2014 has an attenuated phenotype, whereas Georgia 2007/1, Russia/Odi-ntsovo_02/14/Boar and POL/2015/Podlaskie are found to be highly virulent (Davies et al, 2017;Nurmoja et al, 2017).…”

Increased resolution of African Swine Fever Virus genome patterns based on profile HMM protein domains

“…Of potential importance to disease status, it has been observed in several analyses that changes in MGF numbers might result in altered viral properties. A deletion of a large 5' region including multiple MGF_110 elements was associated with attenuation of an Estonian ASFV strain (37). Two GI viruses Lisboa60 (L60, KM262844, a virulent strain) and NH/P68 (NHV, KM262845, a non-virulent strain) studied for their differences in virulence revealed differences in 4 MGF families (MGF_100, MGF_110, MGF_360, MGF_505 (38).…”

“…For example, a naturally-occurring ASFV variant was recently described from Estonia that displayed attenuation in animal tests (37). The original report noted that the Estonian variant was missing 26 genes including 13 members of the MGF_110 family, 3 members of the MGF_360 family, deletions of MGF_100_1R, L83L, L60L and KP177R as well as a duplication and rearrangements (37).…”

“…For example, a naturally-occurring ASFV variant was recently described from Estonia that displayed attenuation in animal tests (37). The original report noted that the Estonian variant was missing 26 genes including 13 members of the MGF_110 family, 3 members of the MGF_360 family, deletions of MGF_100_1R, L83L, L60L and KP177R as well as a duplication and rearrangements (37). We applied the domain classification tool to compare the variant Estonian strain to contemporary viruses from Georgia, changes in protein domains are shown in Figure 5A with domains showing variation across the set of four related genomes indicated by changes in the cluster map.…”