First detection of recombinant variant of African swine fever  virus in the Russian Federation (brief communication)

A. S. Igolkin; R. S. Chernyshev; N. G. Zinyakov; E. O. Morozova; A. R. Shotin; K. N. Gruzdev; I. A. Chvala; A. Mazloum

doi:10.29326/2304-196X-2024-13-3-298-300

First detection of recombinant variant of African swine fever virus in the Russian Federation (brief communication)

A. S. Igolkin, R. S. Chernyshev, N. G. Zinyakov, E. O. Morozova, A. R. Shotin, K. N. Gruzdev, I. A. Chvala, A. Mazloum

https://doi.org/10.29326/2304-196X-2024-13-3-298-300

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Abstract

As part of extensive molecular and genetic research into African swine fever virus isolates circulating in Russia, a recombinant variant with a mosaic genome structure has been identified. The one that caused an outbreak on a pig farm in the Primorsky Krai, in 2023. The characterized strain ASFV/Primorsky_2023/DP-4560.Recdemonstrates hemadsorption, active propagation in porcine primary macrophage cell culture, 99.9917% identity with the first recombinant isolates from the People’s Republic of China, recovered in 2021. Recombination sites included 79 open reading frames homologous to genotype II isolates; 49 ones homologous to genotype I and 12 mixed ones. Testing biomaterial from dead pigs in real-time polymerase chain reaction showed no changes in sensitivity or specificity, despite significant genetic distinctions between the recombinant and genotype II isolates that are enzootic to the Russian Federation. However, in 2023, D. Zhao et al. reported on high virulence of the virus related variants as revealed by the challenge tests in domestic pigs. Given the accelerating rates of AFSV molecular evolution in the East Asian countries (China, Vietnam and the Far Eastern regions of Russia), it is required to improve control measures, general and specific prevention, national and international surveillance over the economically significant animal disease.

Keywords

African swine fever, recombinant variant, genotype I, genotype II, the Primorsky Krai, the Far East

For citations:

Igolkin A.S., Chernyshev R.S., Zinyakov N.G., Morozova E.O., Shotin A.R., Gruzdev K.N., Chvala I.A., Mazloum A. First detection of recombinant variant of African swine fever virus in the Russian Federation (brief communication). Veterinary Science Today. 2024;13(3):298-300. https://doi.org/10.29326/2304-196X-2024-13-3-298-300

In 2023, African swine fever situation (ASF) in Russia was unfavourable. The ASF outbreaks were detected in populations of wild boars and domestic pigs both in backyards and on commercial pig farms in a number of subjects of the Russian Federation.

As part of the research project implemented by the Federal Centre for Animal Health, ASF virus isolate (ASFV/Primorsky_2023/DP-4560.Rec), recovered from an outbreak reported on a commercial pig farm in the Primorsky Krai (in May 2023; Settlement Pervomayskoye, Raion Mikhailovsky), was subjected to a comprehensive sequencing and phylogenetic analysis.

The obtained results were compared with the data from the open sources describing isolates recovered in 2018–2023 in the Primorsky Krai and other subjects of the Russian Federation. As reference samples we used sequences of ASFV genotypes I and II strains from the GenBank international database (i.e. OURT 88/3 – No. AM712240.1 strain and Georgia 2007/1 – No. FR682468.2 strain, respectively), as well as sequences of recombinant isolates (genotypes I and II) detected during ASF outbreaks in 2021–2022 in domestic pigs in the Provinces of Hainan, Inner Mongolia and Jiangsu (China) [1].

During the research, we identified ASF virus that is able to accumulate in porcine bone marrow cell culture at a titer of (8.2 ± 0.23) lg HAD₅₀/cm³, demonstrating the phenomenon of hemadsorption.

Genome-wide sequencing of ASFV/Primorsky_2023/DP-4560.Rec and ASFV/Pig/Jiangsu/LG_China/2021 (recombinant variant registered in China in 2021) isolates demonstrated 99.9917% homology (Fig. 1).

Results of the genome-wide comparison of phylogenetic trees given in Figure 2 clearly demonstrate correspondence of the studied virus from the Primorsky Krai to a separate clade of recombinant isolates from China (2021–2022).

Formation of the recombination sites (79 open reading frames (ORF) belong to genotype II, 49 to genotype I, 12 are mixed) in the genome of ASFV/Primorsky_2023/DP-4560.Rec strain are shown in Figure 3.

The recombinant variant described by D. Zhao et al. in 2023 was characterized as highly virulent for domestic pigs [1]. It was also reported that pilot ASF vaccines manufactured from HLJ/18-7GD strain (developed by Harbin Veterinary Research Institute), protect from virulent genotype II virus but do not protect pigs from infection with the recombinant variant [2].

In 2023, the recombinant virus variant, similar to the previous ones, was detected in the northern provinces of Vietnam [3].

Currently, the Federal Centre for Animal Health researchers are studying biological properties of ASFV/Primorsky_2023/DP-4560.Rec isolate, testing its properties in susceptible animals as well. Primary data suggest that the genome changes do not affect sensitivity and specificity of real-time polymerase chain reaction, which is widely used to diagnose the disease. The results of further and ongoing experiments will be reported additionally.

Fig. 1. Genome-wide map showing correspondence of sequences between ASF isolates ASFV/Primorsky_2023/DP-4560.Rec and ASFV/Pig/Jiangsu/LG_China/2021 (blue color shows homology between the sequences)

Fig. 2. Phylogenetic tree of ASFV/Primorsky_2023/DP-4560.Rec (●) and other ASF virus strains

Fig. 3. Map of the annotated ORFs in ASFV/Primorsky_2023/DP-4560.Rec strain (ORFs with a high percentage of identity to genotype II sequence are given in purple; ORFs similar to genotype I are given in green; genes having sequence identical with genotype II, but mutations identical to genotype I are given in orange)

CONCLUSION

The data obtained re-confirm ASF transboundary nature, demonstrate vulnerability of the global pig industry and set up new requirements for vaccines being developed against this disease.

References

1. Zhao D., Sun E., Huang L., Ding L., Zhu Y., Zhang J., et al. Highly lethal genotype I and II recombinant African swine fever viruses detected in pigs. Nature Communications. 2023; 14:3096. https://doi.org/10.1038/s41467-023-38868-w

2. Chen W., Zhao D., He X., Liu R., Wang Z., Zhang X., et al. A seven-genedeleted African swine fever virus is safe and effective as a live attenuated vaccine in pigs. Science China Life Sciences. 2020; 63 (5): 623–634. https://doi.org/10.1007/s11427-020-1657-9

3. Le V. P., Nguyen V. T., Le T. B., Mai N. T. A., Nguyen V. D., Than T. T., et al. Detection of recombinant African swine fever virus strains of p72 genotypes I and II in domestic pigs, Vietnam, 2023. Emerging Infectious Diseases. 2024; 30 (5): 991–994. https://doi.org/10.3201/eid3005.231775