Comparative genomic and transcriptomic analyses of African swine fever virus strains

Peng Lu; Jiaqiao Zhou; Sibo Wei; Konosuke Takada; Hayato Masutani; Suguru Okuda; Ken Okamoto; Michio Suzuki; Tomoya Kitamura; Kentaro Masujin; Takehiro Kokuho; Hideaki Itoh; Koji Nagata

Computational and Structural Biotechnology Journal (Jan 2023)

Comparative genomic and transcriptomic analyses of African swine fever virus strains

Peng Lu,
Jiaqiao Zhou,
Sibo Wei,
Konosuke Takada,
Hayato Masutani,
Suguru Okuda,
Ken Okamoto,
Michio Suzuki,
Tomoya Kitamura,
Kentaro Masujin,
Takehiro Kokuho,
Hideaki Itoh,
Koji Nagata

Affiliations

Peng Lu: Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
Jiaqiao Zhou: Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
Sibo Wei: Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
Konosuke Takada: Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
Hayato Masutani: Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
Suguru Okuda: Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
Ken Okamoto: Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
Michio Suzuki: Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
Tomoya Kitamura: African Swine Fever Unit, National Institute of Animal Health, National A griculture and Food Research Organization (NARO), 6-20-1 Josuihoncho, Kodaira, Tokyo, Japan
Kentaro Masujin: African Swine Fever Unit, National Institute of Animal Health, National A griculture and Food Research Organization (NARO), 6-20-1 Josuihoncho, Kodaira, Tokyo, Japan
Takehiro Kokuho: African Swine Fever Unit, National Institute of Animal Health, National A griculture and Food Research Organization (NARO), 6-20-1 Josuihoncho, Kodaira, Tokyo, Japan
Hideaki Itoh: Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
Koji Nagata: Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; Corresponding author at: Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.

Journal volume & issue: Vol. 21
pp. 4322 – 4335

Abstract

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African swine fever (ASF) is the most devastating disease caused by the African swine fever virus (ASFV), impacting the pig industry worldwide and threatening food security and biodiversity. Although two vaccines have been approved in Vietnam to combat ASFV, the complexity of the virus, with its numerous open reading frames (ORFs), necessitates a more diverse vaccine strategy. Therefore, we focused on identifying and investigating the potential vaccine targets for developing a broad-spectrum defense against the virus. This study collected the genomic and/or transcriptomic data of different ASFV strains, specifically from in vitro studies, focusing on comparisons between genotypes I, II, and X, from the National Center for Biotechnology Information (NCBI) database. The comprehensive analysis of the genomic and transcriptomic differences between high- and low-virulence strains revealed six early genes, 13 late genes, and six short genes as potentially essential ORFs associated with high-virulence. In addition, many other ORFs (e.g., 14 multigene family members) are worth investigating. The results of this study provided candidate ORFs for developing ASF vaccines and therapies.

Published in Computational and Structural Biotechnology Journal

ISSN: 2001-0370 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Technology: Chemical technology: Biotechnology
Website: https://www.journals.elsevier.com/computational-and-structural-biotechnology-journal

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