Bayesian Phylodynamic Analysis Reveals the Dispersal Patterns of African Swine Fever Virus

Shen, Zhao-Ji; Ji, Hong; Xie, Chun-Di; Shagainar, Jurmt; Zheng, Feng; Zhang, Xiaodong; Li, Kui; Zhou, Rong

doi:10.3390/v14050889

Cited by 7 publications

(6 citation statements)

References 62 publications

(68 reference statements)

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“…Te genome-wide genome similarity between ASFV genotype I and genotype II ranges between 82.4-94.7%. A few molecular epidemiology studies based on genome sequences have been conducted to reconstruct the evolution of ASFV globally or to trace the origin and evolution of genotype I ASFV in Sardinia [24][25][26]. Up to date, the evolutionary dynamics of genotype II ASFV, currently widespread in Eurasia remain unclear.…”

Section: Introductionmentioning

confidence: 99%

Tracing the Origin of Genotype II African Swine Fever Virus in China by Genomic Epidemiology Analysis

Zhang

Wang

Zhu

et al. 2023

Transboundary and Emerging Diseases

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The pandemic spread of African swine fever (ASF) has caused serious effects on the global pig industry. Virus genome sequencing and genomic epidemiology analysis play an important role in tracking the outbreaks of the disease and tracing the transmission of the virus. Here we obtained the full-length genome sequence of African swine fever virus (ASFV) in the first outbreak of ASF in China on August 3rd, 2018 and compared it with other published genotype II ASFV genomes including 9 genomes collected in China from September 2018 to October 2020. Phylogenetic analysis on genomic sequences revealed that genotype II ASFV has evolved into different genetic clusters with temporal and spatial correlation since being introduced into Europe and then Asia. There was a strong support for the monophyletic grouping of all the ASFV genome sequences from China and other Asian countries, which shared a common ancestor with those from the Central or Eastern Europe. An evolutionary rate of 1.312 × 10−5 nucleotide substitutions per site per year was estimated for genotype II ASFV genomes. Eight single nucleotide variations which located in MGF110-1L, MGF110-7L, MGF360-10L, MGF505-5R, MGF505-9R, K145R, NP419L, and I267L were identified as anchor mutations that defined genetic clusters of genotype II ASFV in Europe and Asia. This study expanded our knowledge of the molecular epidemiology of ASFV and provided valuable information for effective control of the disease.

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Section: Introductionmentioning

confidence: 99%

Tracing the Origin of Genotype II African Swine Fever Virus in China by Genomic Epidemiology Analysis

Zhang

Wang

Zhu

et al. 2023

Transboundary and Emerging Diseases

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“…Different types of ASFV genome variation have been identified including the gain or loss of MGF members, deletion or insertion of genomic fragments, variation in the numbers of repeat units in the tandem repeat sequences, polymer tract variation and single nucleotide variation. Molecular epidemiology studies based on genome sequences have been conducted to reconstruct the evolution of ASFV globally or trace the origin and evolution of genotype I ASFV in Sardinia [ 21 , 22 , 23 , 24 ]. Genomic epidemiology analysis has demonstrated that genotype II ASFV in Eurasia has evolved into genetic clusters defined by eight anchor mutations [ 25 ].…”

Section: Introductionmentioning

confidence: 99%

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

Shi,

Wang,

Liu

et al. 2024

Viruses

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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.

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“…Similar to other dsDNA viruses, ASFV genome is highly conserved, and nucleotide substitution the main driving force of genomic evolution occurs at extremely slow rate ( Shen et al. 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Origin, genomic diversity and evolution of African swine fever virus in East Asia

Xin,

Kuang,

et al. 2023

Virus Evolution

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Since 2018, the outbreaks of genotype II African swine fever virus (ASFV) in China and several eastern Asian countries has caused a huge impact on the local swine industry, resulting in huge economic losses. However, little is known about the origin, genomic diversity, evolutionary features, and epidemiological history of the genotype II ASFV. Here, 14 high-quality complete genomes of ASFVs were generated via sequencing of samples collected from China over the course of three years, followed by phylogenetic and phylodynamic analyses. The strains identified were relatively homogeneous, with a total of 52 SNPs and 11 indels compared with the prototype strain HLJ/2018, among which there were four exceptionally large deletions (620–18,023 nt). Evolutionary analyses revealed that ASFV strains distributed in eastern Asia formed a monophyly and a “star-like” structure centered around the prototype strain, suggesting a single origin. Additionally, phylogenetic network analysis and ancestral reconstruction of geographic state indicated that genotype II ASFV stains in eastern Asia likely originated from western Europe. Overall, these results contribute to the understanding of the history and current status of genotype II ASFV strains in eastern Asian, which could be of considerable importance in disease control and prevention.

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Bayesian Phylodynamic Analysis Reveals the Dispersal Patterns of African Swine Fever Virus

Cited by 7 publications

References 62 publications

Tracing the Origin of Genotype II African Swine Fever Virus in China by Genomic Epidemiology Analysis

Tracing the Origin of Genotype II African Swine Fever Virus in China by Genomic Epidemiology Analysis

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

Origin, genomic diversity and evolution of African swine fever virus in East Asia

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