Genetic variations of African swine fever virus MGF 505-9R/10R and I73R/I329L intergenic regions: their role in differentiation between recombinant variant and genotype I and II isolates

The onset of a new African swine fever pandemic prompted the development of alternative approaches to national and international surveillance, control, and disease management. One such approach involved the use of molecular epidemiology methods. Because of the high degree of genetic diversity of tandem repeats (TRs) in the I73R/I329L and MGF 505-9R/10R intergenic regions of ASFV genotype II isolates, these genome markers are used in epidemiological studies. In this study, Sanger sequencing was used to analyze the I73R/I329L and MGF 505-9R/10R intergenic regions of 129 Russian ASFV isolates from 2018–2022. The variants IGR-I (3.1%) and IGR-II (96.9%) of the intergenic region I73R/I329L, as well as MGF-I (95.3%), MGF-II (3.9%), and MGF-V (0.8%) of the non-translated fragment MGF 505-9R/10R, were found among the isolates. In addition, based on PCR and Sanger sequencing of the intergenic regions and the B646L fragment, a method for differentiating ASFV genotypes I and II from a recombinant variant circulating in China, Vietnam, and Eastern Russia is proposed. Our study confirms that the I73R/I329L and MGF 505-9R/10R intergenic regions can be used as markers for epidemiological surveillance of ASFV along the borders of the Russian Federation. However, their usefulness in the study of virus circulation might be limited by the tendency for identical TR insertions to occur spontaneously in unrelated isolates from geographically remote regions of Eurasia (e.g., IGR-III in Poland and China; IGR-IV in Poland and Vietnam; MGF-V in Lithuania and Volgograd Region of Russia).