A Whole-Genome Analysis of the African Swine Fever Virus That Circulated during the First Outbreak in Vietnam in 2019 and Subsequently in 2022

Van Phan Le; Min-Ju Ahn; Jun-Seob Kim; Min-Chul Jung; Sun-Woo Yoon; Thi Bich Ngoc Trinh; Thi Ngoc Le; Hye Kwon Kim; Jung-Ah Kang; Jong-Woo Lim; Minjoo Yeom; Woonsung Na; Xing Xie; Zhixin Feng; Daesub Song; Dae Gwin Jeong

doi:10.3390/v15091945

A Whole-Genome Analysis of the African Swine Fever Virus That Circulated during the First Outbreak in Vietnam in 2019 and Subsequently in 2022

Viruses. 2023 Sep 18;15(9):1945. doi: 10.3390/v15091945.

Authors

Van Phan Le¹, Min-Ju Ahn^{2

3}, Jun-Seob Kim⁴, Min-Chul Jung^{2

3}, Sun-Woo Yoon⁵, Thi Bich Ngoc Trinh¹, Thi Ngoc Le^{2

3}, Hye Kwon Kim⁶, Jung-Ah Kang³, Jong-Woo Lim⁷, Minjoo Yeom⁷, Woonsung Na⁸, Xing Xie⁹, Zhixin Feng⁹, Daesub Song⁷, Dae Gwin Jeong^{2

3}

Affiliations

¹ Department of Microbiology and Infectious Diseases, College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi 100000, Vietnam.
² Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, Republic of Korea.
³ Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea.
⁴ Department of Nano-Bioengineering, Incheon National University, Incheon 22012, Republic of Korea.
⁵ Department of Biological Science and Biotechnology, Andong National University, Andong 36729, Republic of Korea.
⁶ Department of Microbiology, College of Natural Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea.
⁷ College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea.
⁸ College of Veterinary Medicine, Chonnam National University, Gwangju 61186, Republic of Korea.
⁹ Key Laboratory for Veterinary Bio-Product Engineering, Ministry of Agriculture and Rural Affairs, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.

Abstract

Since its initial report in Vietnam in early 2019, the African swine fever (ASF), a highly lethal and severe viral swine disease worldwide, continues to cause outbreaks in other Southeast Asian countries. This study analyzed and compared the genomic sequences of ASF viruses (ASFVs) during the first outbreak in Hung Yen (VN/HY/2019-ASFV1) and Quynh Phu provinces (VN/QP/2019-ASFV1) in Vietnam in 2019, and the subsequent outbreak in Hung Yen (VN/HY/2022-ASFV2) in 2022, to those of other ASFV strains. VN/HY/2019-ASFV1, VN/QP/2019-ASFV1, and VN/HY/2022-ASFV2 genomes were 189,113, 189,081, and 189,607 bp in length, encoding 196, 196, and 203 open reading frames (ORFs), respectively. VN/HY/2019-ASFV1 and VN/QP/2019-ASFV1 shared a 99.91-99.99% average nucleotide identity with genotype II strains. Variations were identified in 28 ORFs in VN/HY/2019-ASFV1 and VN/QP/2019-ASFV1 compared to 20 ASFV strains, and 16 ORFs in VN/HY/2022-ASFV2 compared to VN/HY/2019-ASFV1 and VN/QP/2019-ASFV1. Vietnamese ASFV genomes were classified as IGR II variants between the I73R and I329L genes, with two copy tandem repeats between the A179L and A137R genes. A phylogenetic analysis based on the whole genomes of 27 ASFV strains indicated that the Vietnamese ASFV strains are genetically related to Estonia 2014, ASFV-SY18, and Russia/Odintsovo_02/14. These results reveal the complete genome sequences of ASFV circulating during the first outbreak in 2019, providing important insights into understanding the evolution, transmission, and genetic variation of ASFV in Vietnam.

Keywords: African swine fever; complete genome sequence; next-generation sequencing; virus evolution.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

African Swine Fever Virus* / genetics
African Swine Fever* / epidemiology
Animals
Disease Outbreaks
Phylogeny
Swine
Vietnam / epidemiology

Grants and funding

This work was supported by grants from the KRIBB Initiative Program (KGM5182322), a grant from the National Research Foundation of Korea (NRF) funded by the Korean government (grant no. 2019K1A3A1A61091867 and 2020R1C1C1002780), and a Vietnam National Project from Vietnamese government (project code no. DTDL.CN-53/19).