A Novel Spatiotemporal Classification of Eurasian Circulating African Swine Fever Virus Genotype II into Topotypes and Genetic Lineages.

Abstract

African swine fever (ASF) has been a persistent threat to Eurasian pig populations since its emergence in 2007. The disease has become endemic in numerous countries, including Poland, Germany, Romania, Hungary, Italy, the Philippines, and several others. Epidemiological data reveals that over 99% of outbreaks are attributed to a highly virulent hemadsorbing virus belonging to genotype II. Traditional genotyping methods, primarily relying on thegene, have faced significant limitations in providing a comprehensive understanding of virus dissemination patterns. Previous attempts to identify a universal marker for tracking virus spread through analysis of the CVR locus of thegene and thelocus failed to produce a coherent picture of the virus's geographical distribution across Eurasia. To address these challenges, a comprehensive study was conducted involving the analysis of 250 ASFV isolates/strains from 25 countries across Europe and Asia between 2007 and 2024. This research led to the development of a novel sub-genotyping algorithm for ASFV genotype II. The study identified four topotypes: «CAU1», «EU1», «EU2», and «ASIA1». Within these topotypes, 31 genetic lineages were detected, each characterized by specific single-nucleotide polymorphisms (SNPs). Based on the comparison of two methods of sub-genotyping Eurasian ASFVs-the classification by Gallardo C. et al. (2023) based on genetic variations of 6 loci, and the proposed classification into topotypes and genetic lineages using whole-genomes-it was established that the multigenic approach has insufficient resolution. At the same time, significant differences were observed at the level of whole-genomes. The creation of a new spatiotemporal classification has significant applications in international surveillance of ASF outbreaks, local disease monitoring, and investigation of new infection cases.