Improved Strategy for Molecular Characterization of African Swine Fever Viruses from Sardinia, Based on Analysis of p30, CD2V and I73R /I329L Variable Regions

Abstract

African swine fever virus (ASFV) is the aetiological agent of a highly lethal haemorrhagic disease affecting pigs that inflicts significant economic damage on the swine industry. ASF is present in many African countries, in several eastern and central European countries and in Sardinia (Italy). Sequence analyses of variable genomic regions have been extensively used for molecular epidemiological studies of ASFV isolates. Previous sequencing data of genes that codify for viral protein p54, p72 and the central variable region (CVR) within the B602L gene revealed that Sardinian isolates show a very low level of variability. To achieve a finer level of discrimination among such closely related viruses, in this study, we have chosen three different genome regions to investigate the within-genotype relationships and to provide a more accurate assessment of the origin of outbreaks. The analysis of p30 and I73R/I329L sequences obtained from ASFV collected in Sardinia over a 13-years period confirms a remarkable genetic stability in these regions. The sequence comparison of the protein encoded by the EP402R gene (CD2v), carried out on various strains from 1978 to 2014, revealed a temporal subdivision of Sardinian viruses into two subgroups: one group includes the historical isolates from 1978 to 1990, and the second one is comprised of the viruses collected from 1990 until 2014. These data, together with those obtained from CVR within the B602L gene analysis, demonstrated that the viruses circulating in Sardinia belong to p72 genotype I, but have undergone genetic variations in two different regions of the genome since 1990. We proposed the cytoplasmic region of CD2v protein as a new genetic marker that could be use to analyse ASFVs from different locations to track virus spread. Our study reaffirms the need to analyse other genome regions in order to improve the molecular characterization of ASFV.

Epidemiological analyses of African swine fever in the Baltic States and Poland

“…Similarly, based on a sequence comparison with the protein encoded by the EP402R gene, Sanna et al. () observed a temporal division of ASFV strains collected in Sardinia from 1978 to 2014, but no differences in isolates recovered from wild boar and domestic pigs. Critically, Frączyk et al.…”

“…The CD2v transmembrane potential is required for haemadsorption of red blood cells around infected macrophages and for the adhesion of extracellular virions to erythrocytes and consequent viral dissemination. Further, it is known that expression of the CD2v protein enhances virus replication in the tick vector (Sanna et al., ).…”

“…Similarly, Sanna et al. () proposed the CD2v protein as a new genetic marker that could be used to analyse ASFVs from different locations to track virus spread. They did note that whole‐genome sequence analysis could assist in identifying additional ASFV genetic markers capable of discriminating between circulating viruses, thereby facilitating a better understanding of ASFV evolution and epidemiology worldwide.…”

Gaps in African swine fever: Analysis and priorities

“…Closely related ASFV isolates can be distinguished through sequence analysis of tandem repeats in the central variable region within the B602L gene (Gallardo et al., ) or the intergenic region between the I73R and I329L genes at the right end of the genome (Gallardo et al., ). Several other gene regions, such as the E183L encoding p54 protein, the CP204L encoding p30 protein and the protein encoded by the EP402R gene (CD2v), have been proved as useful tools to analyse ASFVs from different locations to track the virus spread (Gallardo et al., ; Gallardo et al., ; Sanna et al., ). The genetic characterization approach is not related to biological properties.…”

Complete Genome Sequence of an African Swine Fever Virus Isolate from Sardinia, Italy

“…Based on nucleotide sequencing of the p72 capsid protein gene, 22 genotypes (I to XXII) have been distinguished, but additional genomic regions have been suggested for increased resolution (2, 3). Genetic analysis of ASFV isolates from Sardinia revealed that they all belong to the p72 genotype I, with only minor variations within the B602L and the EP402R genes (4, 5). To better distinguish between these closely related isolates, comparative analysis of near-full-length or complete viral genome sequences is required.…”