Whole genome sequencing and phylogenetic analysis of African swine fever virus detected in a backyard pig in Mongolia, 2019

Ji-Yeon Hyeon; Erdene-Ochir Tseren-Ochir; Dong-Hun Lee; Sang-Soep Nahm; Douglas P Gladue; Manuel V Borca; Chang-Seon Song; Guillermo R Risatti

doi:10.3389/fvets.2023.1094052

Whole genome sequencing and phylogenetic analysis of African swine fever virus detected in a backyard pig in Mongolia, 2019

Front Vet Sci. 2023 Feb 20:10:1094052. doi: 10.3389/fvets.2023.1094052. eCollection 2023.

Authors

Ji-Yeon Hyeon^{1

2}, Erdene-Ochir Tseren-Ochir³, Dong-Hun Lee², Sang-Soep Nahm², Douglas P Gladue⁴, Manuel V Borca⁴, Chang-Seon Song^{2

5}, Guillermo R Risatti¹

Affiliations

¹ Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CT, United States.
² College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea.
³ Department of Infectious Diseases and Microbiology, School of Veterinary Medicine, Mongolian University of Life Sciences, Ulaanbaatar, Mongolia.
⁴ Plum Island Animal Disease Center, Agriculture Research Service, US Department of Agriculture, Greenport, NY, United States.
⁵ KCAV Co., Ltd., Seoul, Republic of Korea.

Abstract

African swine fever (ASF) is a highly contagious and fatal disease affecting domestic and wild pigs caused by the African swine fever virus (ASFV). Since the first outbreak in China in August 2018, ASF has spread rapidly in Asia. and the first case in Mongolia was confirmed in January 2019. In this study, we report the first whole genome sequence of an ASFV (ASFV SS-3/Mongolia/2019) detected from a backyard pig in Mongolia in February 2019 using whole genome sequencing. We analyzed their phylogenetic relationship with other genotype II ASFVs from Eurasia. The ASFV SS-3/Mongolia/2019 belonged to genotype II (p72 and p54), serogroup 8 (CD2v), Tet-10a variant (pB602L), and IGRIII variant (intergenic region between the I73R/I329L genes). A total of five amino acid substitutions were observed in MGF 360-10L, MGF 505-4R, MGF 505-9R, NP419L, and I267L genes compared to the ASFV Georgia 2007/1 virus. ML phylogenetic analysis of the whole genome sequence showed that the virus shares a high nucleotide sequence identity with ASFVs recently identified in Eastern Europe and Asia and clustered with the ASFV/Zabaykali/WB5314/2020|Russia|2020 virus which was identified at the border between the Russian Federation and Mongolia in 2020. Our results suggest that trans boundary spread of ASF occurred through close geographic proximity.

Keywords: African swine fever (ASF); Mongolia; backyard pig; phylogenetic analysis; whole genome sequencing (WGS).

Grants and funding

J-YH and S-SN are supported by the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, and Forestry (IPET) through the Animal Disease Management Technology Development Program, funded by the Ministry of Agriculture, Food, and Rural Affairs (MAFRA) (122016-02).