African swine fever virus – variants on the rise

Abstract

African swine fever virus (ASFV), a large and complex DNA-virus circulating between soft ticks and indigenous suids in sub-Saharan Africa, has made its way into swine populations from Europe to Asia. This virus, causing a severe haemorrhagic disease (African swine fever) with very high lethality rates in wild boar and domestic pigs, has demonstrated a remarkably high genetic stability for over 10 years. Consequently, analyses into virus evolution and molecular epidemiology often struggled to provide the genetic basis to trace outbreaks while few resources have been dedicated to genomic surveillance on whole-genome level. During its recent incursion into Germany in 2020, ASFV has unexpectedly diverged into five clearly distinguishable linages with at least ten different variants characterized by high-impact mutations never identified before. Noticeably, all new variants share a frameshift mutation in the 3’ end of the DNA polymerase PolX gene O174L, suggesting a causative role as possible mutator gene. Although epidemiological modelling supported the influence of increased mutation rates, it remains unknown how fast virus evolution might progress under these circumstances. Moreover, a tailored Sanger sequencing approach allowed us, for the first time, to trace variants with genomic epidemiology to regional clusters. In conclusion, our findings suggest that this new factor has the potential to dramatically influence the course of the ASFV pandemic with unknown outcome. Therefore, our work highlights the importance of genomic surveillance of ASFV on whole-genome level, the need for high-quality sequences and calls for a closer monitoring of future phenotypic changes of ASFV.

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

“…A sequencing study of an additional 154 samples from WB and DP reported between 2017 and 2020 in Poland determined the additional 14 nt TRS insertion in 50 of the samples ( Figure 6 ) [ 36 ]. A similar insertion was determined in the complete genome sequence of strain Germany/2020, isolated from a wild boar in Germany in 2020, and recently in 19 ASFV samples from Romania [ 28 , 42 ].…”

“…The integration of markers described in genes O174L and K145R is important to evaluate the spread and molecular epidemiology of genotype II ASFVs in Germany, Poland, and other eastern European countries [ 28 , 36 , 42 ].…”

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

“…In contrast, the 2017, 2018 and 2021 Romanian viruses belong to variant I. Except in Germany ( 27 ) the O174L variant II has not been described in other European and Asian countries as it was determined by comparing 254 homologous sequences available at the GenBank.…”

“…Previous sequencing studies of the O174L gene classified the isolates from Poland into two different variants, with variant II being the predominant one in the western part of the country and responsible for the ASF outbreaks in Germany ( 15 , 16 , 27 ). In our study, sequencing of the O174L gene revealed the presence of the O174L -II variant in Poland, as expected, but also in Romania, both in wild boar and domestic pigs.…”

“…However, in Lithuania, Estonia, and Latvia, where the disease has also been endemic since 2014, group 3 detected in the initial outbreaks was clearly the predominant one, with additional spatially and geographically restricted groups. Forth et al ( 27 ) has recently described an increased mutation rate in the affected region of Germany, where the disease was introduced in 2020. Twenty-two ASFV isolates from Germany diverged into five clearly distinguishable lineages with at least 10 different variants characterized by high-impact mutations.…”