Target capture sequencing for the first Nigerian genotype I ASFV genome

Adeniyi C. Adeola; Pam D. Luka; Xiang-Xiang Jiang; Zheng-Fei Cai; Olufunke O. Oluwole; Xian Shi; Bukola M. Oladele; Temilola O. Olorungbounmi; Bamidele Boladuro; Oladipo Omotosho; Victor M. O. Okoro; Philip M. Dawuda; Sunday C. Olaogun; Oscar J. Sanke; Hai-Bing Xie; Richard P. Bishop; Jianlin Han; Jianbo Li; Ya-Ping Zhang; Min-Sheng Peng

doi:10.1099/mgen.0.001069

Target capture sequencing for the first Nigerian genotype I ASFV genome

Adeniyi C. Adeola^1,2,3, Pam D. Luka⁴, Xiang-Xiang Jiang^1,5, Zheng-Fei Cai^1,6, Olufunke O. Oluwole⁷, Xian Shi^1,8, Bukola M. Oladele⁷, Temilola O. Olorungbounmi⁷, Bamidele Boladuro⁷, Oladipo Omotosho⁹, Victor M. O. Okoro¹⁰, Philip M. Dawuda¹¹, Sunday C. Olaogun⁹, Oscar J. Sanke¹², Hai-Bing Xie¹, Richard P. Bishop¹³, Jianlin Han^13,14, Jianbo Li¹, Ya-Ping Zhang^1,2,6,8 and Min-Sheng Peng^1,2,8
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¹ State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China ² Sino‐Africa Joint Research Center, Chinese Academy of Sciences, Kunming, PR China ³ Centre for Biotechnology Research, Bayero University, Kano, Nigeria ⁴ National Veterinary Research Institute, Vom, Nigeria ⁵ College of Life Sciences, Anhui Normal University, Wuhu, PR China ⁶ State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, PR China ⁷ Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria ⁸ Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, PR China ⁹ Department of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria ¹⁰ Department of Animal Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria ¹¹ Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture Makurdi, Makurdi, Nigeria ¹² Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria ¹³ International Livestock Research Institute (ILRI), Nairobi, Kenya ¹⁴ CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science Chinese Academy of Agricultural Sciences(CAAS), Beijing, PR China
*Correspondence: Min-Sheng Peng, [email protected] *Correspondence: Ya-Ping Zhang, [email protected] *Correspondence: Jianbo Li, [email protected]
Published: 25 July 2023 https://doi.org/10.1099/mgen.0.001069

Abstract

African swine fever (ASF) is a contagious viral disease that affects domestic pigs and wild boars, causing significant economic losses globally. After the first Nigerian outbreak in 1997, there have been frequent reports of ASF in pig-producing regions in the country. To facilitate control, it is important to understand the genotype and phylogenetic relationship of ASF viruses (ASFVs). Recent genetic analysis of Nigerian ASFV isolates has revealed the presence of both genotypes I and II; this is based on analysis of a few selected genes. Phylogenetic analysis of ASFV whole genomes highlights virus origins and evolution in greater depth. However, there is currently no information on the ASFV genome from Nigerian isolates. Two ASFV-positive samples were detected during a random survey of 150 Nigerian indigenous pig samples collected in 2016. We assembled near-complete genomes of the two ASFV-positive samples using in-solution hybrid capture sequencing. The genome-wide phylogenetic tree assigned these two genomes into p72 genotype I, particularly close to the virulent Benin 97/1 strain. The two ASFVs share 99.94 and 99.92 % genomic sequence identity to Benin97/1. This provides insight into the origin and relationship of ASFV strains from Nigeria and Italy. The study reports for the first time the determination of near-complete genomes of ASFV using in-solution hybrid capture sequencing, which represents an important advance in understanding the global evolutionary landscape of ASFVs.

Received: 03/05/2023
Accepted: 20/06/2023
Published Online: 25/07/2023

Keyword(s): African swine fever virus (ASFV) , genome , genotype I , Nigeria , phylogeny and target capture sequencing

Funding

This study was supported by the:

Sino-Africa Joint Research Center, Chinese Academy of Sciences (Award SAJC202103)
- Principle Award Recipient: Ya-PingZhang
Key Technologies Research and Development Program (Award 2022YFC2601604)
- Principle Award Recipient: Ya-PingZhang

This is an open-access article distributed under the terms of the Creative Commons Attribution License.

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/content/journal/mgen/10.1099/mgen.0.001069

Target capture sequencing for the first Nigerian genotype I ASFV genome

M Gen 9, 001069 (2023); https://doi.org/10.1099/mgen.0.001069

/content/journal/mgen/10.1099/mgen.0.001069

Microbial Genomics

Volume 9, Issue 7

Short Communication

Open Access

Target capture sequencing for the first Nigerian genotype I ASFV genome

Abstract

Funding

Supplementary material 1

Supplementary material 2

Supplementary material 3

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