scholarly journals A Deeper Insight into Evolutionary Patterns and Phylogenetic History of ASFV Epidemics in Sardinia (Italy) through Extensive Genomic Sequencing

Viruses ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 1994
Author(s):  
Mariangela Stefania Fiori ◽  
Daria Sanna ◽  
Fabio Scarpa ◽  
Matteo Floris ◽  
Antonello Di Nardo ◽  
...  
Keyword(s):  
African Swine Fever Virus ◽  
Phylogenetic Reconstruction ◽  
African Swine Fever ◽  
Control Measures ◽  
Genomic Diversity ◽  
Economic Losses ◽  
Small Scale ◽  
Whole Genome ◽  
Evolutionary Patterns ◽  
Genetic Substructure

African swine fever virus (ASFV) is the etiological agent of the devastating disease African swine fever (ASF), for which there is currently no licensed vaccine or treatment available. ASF is defined as one of the most serious animal diseases identified to date, due to its global spread in regions of Africa, Europe and Asia, causing massive economic losses. On the Italian island of Sardinia, the disease has been endemic since 1978, although the last control measures put in place achieved a significant reduction in ASF, and the virus has been absent from circulation since April 2019. Like many large DNA viruses, ASFV mutates at a relatively slow rate. However, the limited availability of whole-genome sequences from spatial-localized outbreaks makes it difficult to explore the small-scale genetic structure of these ASFV outbreaks. It is also unclear if the genetic variability within outbreaks can be captured in a handful of sequences, or if larger sequencing efforts can improve phylogenetic reconstruction and evolutionary or epidemiological inference. The aim of this study was to investigate the phylogenetic patterns of ASFV outbreaks between 1978 and 2018 in Sardinia, in order to characterize the epidemiological dynamics of the viral strains circulating in this Mediterranean island. To reach this goal, 58 new whole genomes of ASFV isolates were obtained, which represents the largest ASFV whole-genome sequencing effort to date. We provided a complete description of the genomic diversity of ASFV in terms of nucleotide mutations and small and large indels among the isolates collected during the outbreaks. The new sequences capture more than twice the genomic and phylogenetic diversity of all the previously published Sardinian sequences. The extra genomic diversity increases the resolution of the phylogenetic reconstruction, enabling us to dissect, for the first time, the genetic substructure of the outbreak. We found multiple ASFV subclusters within the phylogeny of the Sardinian epidemic, some of which coexisted in space and time.

scholarly journals Genetic Characterization and Variation of African Swine Fever Virus China/GD/2019 Strain in Domestic Pigs

Pathogens ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 97
Author(s):  
Xun Wang ◽  
Xiaoying Wang ◽  
Xiaoxiao Zhang ◽  
Sheng He ◽  
Yaosheng Chen ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Synonymous Mutation ◽  
Nucleotide Polymorphisms ◽  
Mutation Site ◽  
New Variant ◽  
Genotype Ii

African swine fever (ASF) was first introduced into Northern China in 2018 and has spread through China since then. Here, we extracted the viral DNA from the blood samples from an ASF outbreak farm in Guangdong province, China and sequenced the whole genome. We assembled the full length genomic sequence of this strain, named China/GD/2019. The whole genome was 188,642 bp long (terminal inverted repeats and loops were not sequenced), encoding 175 open reading frames (ORF). The China/GD/2019 strain belonged to p72 genotype II and p54 genotype IIa. Phylogenetic analysis relationships based on single nucleotide polymorphisms (SNPs) also demonstrated that it grouped into genotype II. A certain number of ORFs mainly belonging to multigene families (MGFs) were absent in the China/GD/2019 strain in comparison to the China/ASFV/SY-18 strain. A deletion of approximately 1 kb was found in the China/GD/2019 genome which was located at the EP153R and EP402R genes in comparison to the China/2018/AnhuiXCGQ strain. We revealed a synonymous mutation site at gene F317L and a non-synonymous mutation site at gene MGF_360-6L in China/GD/2019 comparing to three known Chinese strains. Pair-wise comparison revealed 165 SNP sites in MGF_360-1L between Estonia 2014 and the China/GD/2019 strain. Comparing to China/GD/2019, we revealed a base deletion located at gene D1133L in China/Pig/HLJ/2018 and China/DB/LN/2018, which results in a frameshift mutation to alter the encoding protein. Our findings indicate that China/GD/2019 is a new variant with certain deletions and mutations. This study deepens our understanding of the genomic diversity and genetic variation of ASFV.

scholarly journals Computational Analysis of African Swine Fever Virus Protein Space for the Design of an Epitope-Based Vaccine Ensemble

Pathogens ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1078 ◽  
Author(s):  
Albert Ros-Lucas ◽  
Florencia Correa-Fiz ◽  
Laia Bosch-Camós ◽  
Fernando Rodriguez ◽  
Julio Alonso-Padilla
Keyword(s):  
T Cell ◽  
Vaccine Development ◽  
De Novo ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Economic Losses ◽  
Virus Protein ◽  
Hemorrhagic Disease ◽  
Starting Point

African swine fever virus is the etiological agent of African swine fever, a transmissible severe hemorrhagic disease that affects pigs, causing massive economic losses. There is neither a treatment nor a vaccine available, and the only method to control its spread is by extensive culling of pigs. So far, classical vaccine development approaches have not yielded sufficiently good results in terms of concomitant safety and efficacy. Nowadays, thanks to advances in genomic and proteomic techniques, a reverse vaccinology strategy can be explored to design alternative vaccine formulations. In this study, ASFV protein sequences were analyzed using an in-house pipeline based on publicly available immunoinformatic tools to identify epitopes of interest for a prospective vaccine ensemble. These included experimentally validated sequences from the Immune Epitope Database, as well as de novo predicted sequences. Experimentally validated and predicted epitopes were prioritized following a series of criteria that included evolutionary conservation, presence in the virulent and currently circulating variant Georgia 2007/1, and lack of identity to either the pig proteome or putative proteins from pig gut microbiota. Following this strategy, 29 B-cell, 14 CD4+ T-cell and 6 CD8+ T-cell epitopes were selected, which represent a starting point to investigating the protective capacity of ASFV epitope-based vaccines.

scholarly journals Risk of African swine fever virus introduction into the United States through smuggling of pork in air passenger luggage

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Cristina Jurado ◽  
Lina Mur ◽  
María Sol Pérez Aguirreburualde ◽  
Estefanía Cadenas-Fernández ◽  
Beatriz Martínez-López ◽  
...  
Keyword(s):  
Western Europe ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
The United States ◽  
Economic Losses ◽  
Swine Industry ◽  
Virus Surveillance ◽  
Global Epidemiology ◽  
The Us ◽  
Mean Risk

Abstract African swine fever causes substantial economic losses in the swine industry in affected countries. Traditionally confined to Africa with only occasional incursions into other regions, ASF began spreading into Caucasian countries and Eastern Europe in 2007, followed by Western Europe and Asia in 2018. Such a dramatic change in the global epidemiology of ASF has resulted in concerns that the disease may continue to spread into disease-free regions such as the US. In this study, we estimated the risk of introduction of ASF virus into the US through smuggling of pork in air passenger luggage. Results suggest that the mean risk of ASFV introduction into the US via this route has increased by 183.33% from the risk estimated before the disease had spread into Western Europe or Asia. Most of the risk (67.68%) was associated with flights originating from China and Hong Kong, followed by the Russian Federation (26.92%). Five US airports accounted for >90% of the risk. Results here will help to inform decisions related to the design of ASF virus surveillance strategies in the US.

scholarly journals Development of a Directly Visualized Recombinase Polymerase Amplification–SYBR Green I Method for the Rapid Detection of African Swine Fever Virus

2020 ◽  
Vol 11 ◽  
Author(s):  
Shuai Zhang ◽  
Aijun Sun ◽  
Bo Wan ◽  
Yongkun Du ◽  
Yanan Wu ◽  
...  
Keyword(s):  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Sybr Green ◽  
Fever Virus ◽  
Diagnostic Methods ◽  
Sybr Green I ◽  
Recombinase Polymerase Amplification ◽  
Economic Losses ◽  
Field Samples ◽  
Standard Plasmid

African swine fever (ASF) is a lethal disease in swine caused by etiologic African swine fever virus (ASFV). The global spread of ASFV has resulted in huge economic losses globally. In the absence of effective vaccines or drugs, pathogen surveillance has been the most important first-line intervention to prevent ASF outbreaks. Among numerous diagnostic methods, recombinase polymerase amplification (RPA)-based detection is capable of producing sensitive and specific results without relying on the use of expensive instruments. However, currently used gene-specific, probe-based RPA for ASFV detection is expensive and time-consuming. To improve the efficiency of ASFV surveillance, a novel directly visualized SYBR Green I-staining RPA (RPAS) method was developed to detect the ASFV genome. SYBR Green I was added to the amplified RPA products for direct visualization by the naked eye. The sensitivity and specificity of this method were confirmed using standard plasmid and inactivated field samples. This method was shown to be highly specific with a detection limit of 103 copies/μl of ASFV in 15 min at 35°C without any cross-reactions with other important porcine viruses selected. In summary, this method enables direct sample visualization with reproducible results for ASFV detection and hence has the potential to be used as a robust tool for ASF prevention and control.

scholarly journals A Simple Method for Sample Preparation to Facilitate Efficient Whole-Genome Sequencing of African Swine Fever Virus

Viruses ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 1129 ◽  
Author(s):  
Ferenc Olasz ◽  
István Mészáros ◽  
Szilvia Marton ◽  
Győző L. Kaján ◽  
Vivien Tamás ◽  
...  
Keyword(s):  
Sample Preparation ◽  
African Swine Fever Virus ◽  
Animal Health ◽  
African Swine Fever ◽  
Fever Virus ◽  
Whole Genome ◽  
Swine Industry ◽  
Viral Dna ◽  
Simple Method ◽  
Generation Sequencing

In the recent years, African swine fever has become the biggest animal health threat to the swine industry. To facilitate quick genetic analysis of its causative agent, the African swine fever virus (ASFV), we developed a simple and efficient method for next generation sequencing of the viral DNA. Execution of the protocol does not demand complicated virus purification steps, enrichment of the virus by ultracentrifugation or of the viral DNA by ASFV-specific PCRs, and minimizes the use of Sanger sequencing. Efficient DNA-se treatment, monitoring of sample preparation by qPCR, and whole genome amplification are the key elements of the method. Through detailed description of sequencing of the first Hungarian ASFV isolate (ASFV_HU_2018), we specify the sensitive steps and supply key reference numbers to assist reproducibility and to facilitate the successful use of the method for other ASFV researchers.

DNA segments of African Swine Fever Virus detected for the first time in hard ticks from sheep and bovines

2019 ◽  
Vol 24 (1) ◽  
pp. 180 ◽  
Author(s):  
Ze Chen ◽  
Xiaofeng Xu ◽  
Yufeng Wang ◽  
Jinlong Bei ◽  
Xiufeng Jin ◽  
...  
Keyword(s):  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Control Measures ◽  
Single Amino Acid ◽  
Small Rna Sequencing ◽  
Hard Ticks ◽  
Prevention And Control Measures ◽  
And Control ◽  
First Time

In this study, we detected African Swine Fever Virus (ASFV) in Dermacentor (Ixodidae) from sheep and bovines using small RNA sequencing. To validate this result, a 235-bp DNA segment was detected in a number of DNA samples from D. silvarum and sheep blood. This 235-bp segment had an identity of 99% to a 235-bp DNA segment of ASFV and contained three single nucleotide mutations (C38T, C76T and A108C). C38T, resulting in a single amino acid mutation G66D, suggests the existence of a new ASFV strain, which is different from all reported ASFV strains in the NCBI GenBank database and the ASFV strain (GenBank: MH713612.1) reported in China in 2018. To further confirm the existence of ASFV in Dermacentor ticks, three DNA segments of ASFV were detected in D. niveus females from bovines and their first generation ticks reared in our lab. These results also proved that transovarian transmission of ASFV occurs in hard ticks. This study revealed for the first time that ASFV has a wider range of hosts (e.g. sheep and bovines) and vectors (e.g. hard ticks), beyond the well-known Suidae family and Argasidae (soft ticks). Our findings pave the way toward further studies on ASFV transmission and the development of prevention and control measures.

scholarly journals Comparative Analysis of Whole-Genome Sequence of African Swine Fever Virus Belgium 2018/1

2019 ◽  
Vol 25 (6) ◽  
pp. 1249-1252 ◽  
Author(s):  
Jan H. Forth ◽  
Marylène Tignon ◽  
Ann Brigitte Cay ◽  
Leonie F. Forth ◽  
Dirk Höper ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Genome Sequence ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Whole Genome Sequence ◽  
Whole Genome

scholarly journals Genetic characterisation of African swine fever virus from 2017 outbreaks in Zambia: Identification of p72 genotype II variants in domestic pigs

2018 ◽  
Vol 85 (1) ◽  
Author(s):  
Edgar Simulundu ◽  
Yona Sinkala ◽  
Herman M. Chambaro ◽  
Andrew Chinyemba ◽  
Frank Banda ◽  
...  
Keyword(s):  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Variable Region ◽  
Economic Losses ◽  
African Region ◽  
Swine Industry ◽  
African Countries ◽  
Central Variable Region ◽  
Close Relationship ◽  
Haemorrhagic Disease

African swine fever (ASF) is a contagious haemorrhagic disease associated with causing heavy economic losses to the swine industry in many African countries. In 2017, Zambia experienced ASF outbreaks in Mbala District (Northern province) and for the first time in Isoka and Chinsali districts (Muchinga province). Meanwhile, another outbreak was observed in Chipata District (Eastern province). Genetic analysis of part of the B646L gene, E183L gene, CP204L gene and the central variable region of the B602L gene of ASF virus (ASFV) associated with the outbreaks in Mbala and Chipata districts was conducted. The results revealed that the ASFV detected in Mbala District was highly similar to that of the Georgia 2007/1 isolate across all the genome regions analysed. In contrast, while showing close relationship with the Georgia 2007/1 virus in the B646L gene, the ASFV detected in Chipata District showed remarkable genetic variation in the rest of the genes analysed. These results suggest that the Georgia 2007/1-like virus could be more diverse than what was previously thought, underscoring the need of continued surveillance and monitoring of ASFVs within the south-eastern African region to better understand their epidemiology and the relationships between outbreaks and their possible origin.

scholarly journals The potential anti- African Swine Fever Virus effects of medium chain fatty acids on in vitro pig feed and water models

2020 ◽  
Author(s):  
Ha Thi Thanh Tran ◽  
Anh Duc Truong ◽  
Duc Viet Ly ◽  
Tuan Van Hoang ◽  
Chinh Thi Nguyen ◽  
...  
Keyword(s):  
Fatty Acids ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Control Measures ◽  
Effective Control ◽  
Medium Chain ◽  
Medium Chain Fatty Acids ◽  
Water Models ◽  
Chain Fatty Acids

Abstract Background African swine fever (ASF) is an important disease affecting swine and has a significant economic loss on both the developed and developing world but due to the lack of vaccines, drug, and effective control measures, ASF virus remains a serious threat to global pork production. The activities of medium-chain fatty acids (MCFAs) against viral pathogens have been reported previously. However, the effects of this family on ASFV have been not yet investigated. In this study, we evaluated the potential effects of MCFAs in individual and synergistic forms, to prevent and/or reduce ASFV infection using in vitro feed and water models. Results The potential effects of MCFAs, including C8, C6-C8-C10 (1:1:1 ratio) and C8-C10-C12 (1:1:1 ratio) against a field ASFV strain isolated in Red River Delta region of Vietnam were further examined by real-time PCR in in vitro feed and water models. All tested products have shown a strong antiviral effect against ASFV infectivity at doses of 0.375% and 0.5% in both feed and water assays. Interestingly, the synergistic MCFAs have shown clearly their potential activities against ASFV in which at lower dose of 0.25%, pre-treatment with product 2 and 3 induced significant increases at the level of Cq value when compared to positive control and/or product 1 (P < 0.05). Conclusions To our knowledge, it is the first report on in vitro examination of the anti-ASFV activities of the MCFAs. Our findings suggested that all tested products, both individual and synergistic forms of MCFAs, have possessed a strong anti-ASFV effect and this effect is dose- dependence in in vitro feed and water models. Additionally, synergistic effects of MCFAs are more effective against ASFV when compared to individual form. The further studies focusing on in vivo anti-ASFV effects of MCFAs are very important to bring new insight into the mode of ASFV-reduced action by these compounds in swine feed and water consumption.

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