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Volume 16
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10.3390/v16020312
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Article

Generation of High-Quality African Swine Fever Virus Complete Genome from Field Samples by Next-Generation Sequencing

by
Chuan Shi
1,2,3,†,
Qinghua Wang
1,†,
Yutian Liu
1,
Shujuan Wang
1,
Yongqiang Zhang
1,
Chunju Liu
1,
Yongxin Hu
1,
Dongxia Zheng
1,
Chengyou Sun
1,
Fangfang Song
1,
Xiaojing Yu
1,
Yunling Zhao
1,
Jingyue Bao
1,* and
Zhiliang Wang
1,*
1
China Animal Health and Epidemiology Center, Qingdao 266032, China
2
BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
3
College of Life Sciences, University of Chinese Academy of Sciences, Beijing 518083, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Viruses 2024, 16(2), 312; https://doi.org/10.3390/v16020312
Submission received: 25 December 2023 / Revised: 12 February 2024 / Accepted: 12 February 2024 / Published: 18 February 2024
(This article belongs to the Special Issue African Swine Fever Virus 4.0)
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Abstract

African swine fever (ASF) is a lethal contagious viral disease of domestic pigs and wild boars caused by the African swine fever virus (ASFV). The pandemic spread of ASF has caused severe effects on the global pig industry. Whole-genome sequencing provides crucial information for virus strain characterization, epidemiology analysis and vaccine development. Here, we evaluated the performance of next-generation sequencing (NGS) in generating ASFV genome sequences from clinical samples. Thirty-four ASFV-positive field samples including spleen, lymph node, lung, liver and blood with a range of Ct values from 14.73 to 25.95 were sequenced. For different tissue samples collected from the same sick pigs, the proportion of ASFV reads obtained from the spleen samples was 3.69–9.86 times higher than other tissues. For the high-viral-load spleen samples (Ct < 20), a minimum of a 99.8% breadth of ≥10× coverage was revealed for all the samples. For the spleen samples with Ct ≥ 20, 6/12 samples had a minimum of a 99.8% breadth of ≥10× coverage. A high average depth of sequencing coverage was also achieved from the blood samples. According to our results, high-quality ASFV whole-genome sequences could be obtained from the spleen or blood samples with Ct < 20. The high-quality ASFV genome sequence generated in this study was further used for the high-resolution phylogenetic analysis of the ASFV genomes in the early stage of the ASF epidemic in China. Our study demonstrates that NGS may act as a useful tool for efficient ASFV genome characterization, providing valuable information for disease control.
Keywords: African swine fever virus; next-generation sequencing; genome characterization; clinical samples African swine fever virus; next-generation sequencing; genome characterization; clinical samples

Share and Cite

MDPI and ACS Style

Shi, C.; Wang, Q.; Liu, Y.; Wang, S.; Zhang, Y.; Liu, C.; Hu, Y.; Zheng, D.; Sun, C.; Song, F.; et al. Generation of High-Quality African Swine Fever Virus Complete Genome from Field Samples by Next-Generation Sequencing. Viruses 2024, 16, 312. https://doi.org/10.3390/v16020312

AMA Style

Shi C, Wang Q, Liu Y, Wang S, Zhang Y, Liu C, Hu Y, Zheng D, Sun C, Song F, et al. Generation of High-Quality African Swine Fever Virus Complete Genome from Field Samples by Next-Generation Sequencing. Viruses. 2024; 16(2):312. https://doi.org/10.3390/v16020312

Chicago/Turabian Style

Shi, Chuan, Qinghua Wang, Yutian Liu, Shujuan Wang, Yongqiang Zhang, Chunju Liu, Yongxin Hu, Dongxia Zheng, Chengyou Sun, Fangfang Song, and et al. 2024. "Generation of High-Quality African Swine Fever Virus Complete Genome from Field Samples by Next-Generation Sequencing" Viruses 16, no. 2: 312. https://doi.org/10.3390/v16020312

APA Style

Shi, C., Wang, Q., Liu, Y., Wang, S., Zhang, Y., Liu, C., Hu, Y., Zheng, D., Sun, C., Song, F., Yu, X., Zhao, Y., Bao, J., & Wang, Z. (2024). Generation of High-Quality African Swine Fever Virus Complete Genome from Field Samples by Next-Generation Sequencing. Viruses, 16(2), 312. https://doi.org/10.3390/v16020312

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