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Genome-Wide Diversity Analysis of African Swine Fever Virus Based on a Curated Dataset
SIMPLE SUMMARY: African swine fever (ASF) is one of the most important animal diseases affecting the domestic swine population globally. Whole-genome sequence analysis on the circulating African swine fever virus (ASFV) strains would provide valuable information in tracking the outbreaks of the dise...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9495133/ https://www.ncbi.nlm.nih.gov/pubmed/36139306 http://dx.doi.org/10.3390/ani12182446 |
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author | Bao, Jingyue Zhang, Yong Shi, Chuan Wang, Qinghua Wang, Shujuan Wu, Xiaodong Cao, Shengbo Xu, Fengping Wang, Zhiliang |
author_facet | Bao, Jingyue Zhang, Yong Shi, Chuan Wang, Qinghua Wang, Shujuan Wu, Xiaodong Cao, Shengbo Xu, Fengping Wang, Zhiliang |
author_sort | Bao, Jingyue |
collection | PubMed |
description | SIMPLE SUMMARY: African swine fever (ASF) is one of the most important animal diseases affecting the domestic swine population globally. Whole-genome sequence analysis on the circulating African swine fever virus (ASFV) strains would provide valuable information in tracking the outbreaks of the disease. The aim of this study was to prepare a curated dataset of ASFV genome sequences and investigate genome-wide diversity of circulating ASFV strains. We prepared a curated dataset containing 123 high-quality ASFV genome sequences representing 10 genotypes collected from 28 countries between 1949 and 2020. Phylogenetic analysis based on whole-genome sequences provided high-resolution topology in genotyping ASFV isolates, which was supported by pairwise genome sequence similarity comparison. Wide distribution and high variation of tandem repeat sequences were found in ASFV genomes. Structural variation and highly variable poly G or poly C tracts were also identified. This study improved our understanding on the patterns of genetic variation of ASFV and facilitated future studies on ASFV molecular epidemiology. 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 had serious effects on the global pig industry. Virus genome sequencing and comparison play an important role in tracking the outbreaks of the disease and tracing the transmission of the virus. Although more than 140 ASFV genome sequences have been deposited in the public databases, the genome-wide diversity of ASFV remains unclear. Here we prepared a curated dataset of ASFV genome sequences by filtering genomes with sequencing errors as well as duplicated genomes. A total of 123 ASFV genome sequences were included in the dataset, representing 10 genotypes collected between 1949 and 2020. Phylogenetic analysis based on whole-genome sequences provided high-resolution topology in differentiating closely related ASFV isolates, and drew new clues in the classification of some ASFV isolates. Genome-wide diversity of ASFV genomes was explored by pairwise sequence similarity comparison and ORF distribution comparison. Tandem repeat sequences were found widely distributed and highly varied in ASFV genomes. Structural variation and highly variable poly G or poly C tracts also contributed to the genome diversity. This study expanded our knowledge on the patterns of genetic diversity and evolution of ASFV, and provided valuable information for diagnosis improvement and vaccine development. |
format | Online Article Text |
id | pubmed-9495133 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-94951332022-09-23 Genome-Wide Diversity Analysis of African Swine Fever Virus Based on a Curated Dataset Bao, Jingyue Zhang, Yong Shi, Chuan Wang, Qinghua Wang, Shujuan Wu, Xiaodong Cao, Shengbo Xu, Fengping Wang, Zhiliang Animals (Basel) Article SIMPLE SUMMARY: African swine fever (ASF) is one of the most important animal diseases affecting the domestic swine population globally. Whole-genome sequence analysis on the circulating African swine fever virus (ASFV) strains would provide valuable information in tracking the outbreaks of the disease. The aim of this study was to prepare a curated dataset of ASFV genome sequences and investigate genome-wide diversity of circulating ASFV strains. We prepared a curated dataset containing 123 high-quality ASFV genome sequences representing 10 genotypes collected from 28 countries between 1949 and 2020. Phylogenetic analysis based on whole-genome sequences provided high-resolution topology in genotyping ASFV isolates, which was supported by pairwise genome sequence similarity comparison. Wide distribution and high variation of tandem repeat sequences were found in ASFV genomes. Structural variation and highly variable poly G or poly C tracts were also identified. This study improved our understanding on the patterns of genetic variation of ASFV and facilitated future studies on ASFV molecular epidemiology. 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 had serious effects on the global pig industry. Virus genome sequencing and comparison play an important role in tracking the outbreaks of the disease and tracing the transmission of the virus. Although more than 140 ASFV genome sequences have been deposited in the public databases, the genome-wide diversity of ASFV remains unclear. Here we prepared a curated dataset of ASFV genome sequences by filtering genomes with sequencing errors as well as duplicated genomes. A total of 123 ASFV genome sequences were included in the dataset, representing 10 genotypes collected between 1949 and 2020. Phylogenetic analysis based on whole-genome sequences provided high-resolution topology in differentiating closely related ASFV isolates, and drew new clues in the classification of some ASFV isolates. Genome-wide diversity of ASFV genomes was explored by pairwise sequence similarity comparison and ORF distribution comparison. Tandem repeat sequences were found widely distributed and highly varied in ASFV genomes. Structural variation and highly variable poly G or poly C tracts also contributed to the genome diversity. This study expanded our knowledge on the patterns of genetic diversity and evolution of ASFV, and provided valuable information for diagnosis improvement and vaccine development. MDPI 2022-09-16 /pmc/articles/PMC9495133/ /pubmed/36139306 http://dx.doi.org/10.3390/ani12182446 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Bao, Jingyue Zhang, Yong Shi, Chuan Wang, Qinghua Wang, Shujuan Wu, Xiaodong Cao, Shengbo Xu, Fengping Wang, Zhiliang Genome-Wide Diversity Analysis of African Swine Fever Virus Based on a Curated Dataset |
title | Genome-Wide Diversity Analysis of African Swine Fever Virus Based on a Curated Dataset |
title_full | Genome-Wide Diversity Analysis of African Swine Fever Virus Based on a Curated Dataset |
title_fullStr | Genome-Wide Diversity Analysis of African Swine Fever Virus Based on a Curated Dataset |
title_full_unstemmed | Genome-Wide Diversity Analysis of African Swine Fever Virus Based on a Curated Dataset |
title_short | Genome-Wide Diversity Analysis of African Swine Fever Virus Based on a Curated Dataset |
title_sort | genome-wide diversity analysis of african swine fever virus based on a curated dataset |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9495133/ https://www.ncbi.nlm.nih.gov/pubmed/36139306 http://dx.doi.org/10.3390/ani12182446 |
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