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

Authors :
Chuan Shi
Qinghua Wang
Yutian Liu
Shujuan Wang
Yongqiang Zhang
Chunju Liu
Yongxin Hu
Dongxia Zheng
Chengyou Sun
Fangfang Song
Xiaojing Yu
Yunling Zhao
Jingyue Bao
Zhiliang Wang
Source :
Viruses, Vol 16, Iss 2, p 312 (2024)
Publication Year :
2024
Publisher :
MDPI AG, 2024.

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.

Details

Language :
English
ISSN :
19994915
Volume :
16
Issue :
2
Database :
Directory of Open Access Journals
Journal :
Viruses
Publication Type :
Academic Journal
Accession number :
edsdoj.f9f1ae79fbf14e81b98ae72668465379
Document Type :
article
Full Text :
https://doi.org/10.3390/v16020312