Molecular Characterization of African Swine Fever Virus Isolates in Estonia in 2014-2019

Genetic analysis reveals multiple intergenic region and central variable region in the African swine fever virus variants circulating in Serbia

This study provides the first comprehensive report on the molecular characteristics of African swine fever virus (ASFV) variants in Serbia between 2019 and 2022. Since its first observation in July 2019, the disease has been found in wild boar and domestic swine. The study involved the analysis of 95 ASFV-positive samples collected from 12 infected administrative districts in Serbia. Partial four genomic regions were genetically characterized, including B646L, E183L, B602L, and the intergenic region (IGR) between the I73R-I329L genes. The results of the study suggest that multiple ASFV strains belonging to genotype II are circulating in Serbia, as evidenced by the analysis of the IGR between I73R-I329L genes that showed the most differences. Furthermore, the phylogenetic analysis of the B602L gene showed three different clades within the CVR I group of ASFV strains. Regarding the IGR, 98.4% were grouped into IGR II, with only one positive sample grouped into the IGR III group. These findings provide essential insights into the molecular characteristics of ASFV variants in Serbia and contribute to the knowledge of circulating strains of ASFV in Europe. However, further research is necessary to gain a better understanding of ASFV spread and evolution.

[Molecular and biological properties of the African swine fever virus (Asfarviridae: Asfivirus) isolate ASF/Tatarstan 20/WB-12276]

INTRODUCTION

Up-to-date data and full characterization of circulating ASFV isolates play a crucial role in virus eradication and control in endemic regions and countries. The aim of the study was to evaluate and characterize the molecular and biological properties of the ASFV isolate ASF/Tatarstan 20/WB-12276, conduct phylogenetic analysis, and compare the results with isolates circulating in Europe and Asia.

MATERIALS AND METHODS

For bioassay, eight heads of the Large White pigs weighing 15-20 kg/head were used. Detection of specific anti-ASFV antibodies by ELISA and immunoperoxidase method. Detection of ASFV genome was performed by qPCR. Isolation of ASF/Tatarstan 20/WB-12276 and determination of titer were performed in pig spleen cell culture. Sequencing was carried out by the Sanger method.

RESULTS

The virus was characterized as highly virulent and capable of causing acute to subacute forms of ASF. Phylogenetic analysis revealed substitutions in the genome of the ASF/Tatarstan 20/WB-12276 isolate (IGR/I73R-I329L and I267L markers) that supported the clustering of the studied variant with isolates prevalent in most of Europe and Asia.

CONCLUSION

For the first time, the molecular and biological properties of the ASF/Tatarstan 20/WB-12276 virus isolate taken from a wild boar shot on the territory of the Republic of Tatarstan were studied and analyzed.

African Swine Fever in Wild Boar: German Hunters' Perception of Surveillance and Control-A Questionnaire Study

Since the first occurrence of African swine fever (ASF) in wild boar in Germany in 2020, the disease has primarily affected the wild boar population in the eastern part of the country close to the border with Poland. Local hunters play a crucial role in implementing surveillance and control. To evaluate their perceptions of existing control measures and analyze regional differences between hunters from ASF-affected and non-affected regions, a questionnaire study was conducted among the German hunting community. Hunters from non-affected areas held a more optimistic view regarding the effectiveness of control measures compared to hunters from affected areas. However, control measures that hinder hunting were generally perceived as ineffective. Measures that collided with hunters' understanding of fair hunting practices were regarded as controversial. Financial incentives and reducing bureaucracy were the most favored approaches to increase hunters' participation. Moreover, the possibility of eating or selling the meat of hunted wild boar and the provision of infrastructure for implementing ASF control were considered motivating. Thus, this study highlights the importance of compensating hunters and addressing their concerns to maintain their engagement in ASF control. To enhance compliance with controversial measures, thoughtful communication and raising awareness are essential.

Genetic Profile of African Swine Fever Viruses Circulating at Pig Farms in South Korea during the Outbreaks between 2022 and April 2023

Fifteen pig farms were affected by African swine fever (ASF) in South Korea during the outbreaks between 2022 and April 2023. The ASF virus (ASFV) genome was directly extracted from the blood and tissue samples of 15 ASFV-positive pig farms to analyze the genetic characteristics. Phylogenetic analysis revealed that the 15 strains belonged to p72 genotype II and CD2v serogroup 8, which were the central variable region (CVR) I variants of the B602L gene. Fourteen strains were intergenic region (IGR) II variants, containing an additional tandem repeat sequence (TRS), between I73L and I329R, with the exception of one strain from an ASFV-infected pig farm reported on 22 January 2023, which was an IGR I variant. In addition, a single-nucleotide polymorphism (SNP) was detected at position 107 from the start of the IGR between A179L and A137R in six isolates. The findings of this study suggest that the sources of the virus at the pig farms from which these variants originated differed from those of other pig farms.

New perspective on African swine fever: a bibliometrics study and visualization analysis

Introduction

African swine fever (ASF) is a contagious viral disease that can have devastating effects on domestic pigs and wild boars. Over the past decade, there has been a new wave of this ancient disease spreading around the world, prompting many scholars to dedicate themselves to researching this disease. This research aims to use bibliometric methods to organize, analyze and summarize the scientific publications on ASF that have been amassed in the past two decades.

Methods

This paper used VOSviewer, CiteSpace, and a bibliometric online analysis platform to conduct performance analysis and visualization studies on 1,885 academic papers about ASF in the Web of Science from January 2003 to December 2022.

Results

The amount of literature published on ASF has increased exponentially in recent years, and the development trend of related research is good. A group of representative scholars have appeared in this research field, and some cooperative networks have been formed. Transboundary and Emerging Diseases is the journal with the most publications in this field, while Virus Research is the journal with the most citation per article. High-productivity countries are led by China in terms of the number of articles published followed by the United States and Spain. In regard to the average number of citations, the scholars in the UK are in the lead. The institution with the most articles was the Chinese Academy of Agricultural Sciences. The analysis of high-frequency keywords showed that the pathogens and epidemiology of ASF were the research hotspots in this field, and the research content was closely related to molecular biology and immunology. The burst keywords "transmission", "identification", "virulence", "replication", and "gene" reflects the research frontier. In addition, by collating and analyzing highly cited journals and highly co-cited references, we explored the knowledge structure and theoretical basis of this field.

Discussion

This is the first bibliometric analysis report on ASF research, which highlights the key characteristics of ASF research and presents the research status and evolution trend in this field from a new perspective. It provides a valuable reference for further research.

Differentiation of African Swine Fever Virus Strains Isolated in Estonia by Multiple Genetic Markers

The African swine fever virus (ASFV) was first detected in Estonia, in September 2014. In the subsequent three years, the virus spread explosively all over the country. Only one county, the island of Hiiumaa, remained free of the disease. Due to the drastic decrease in the wild boar population in the period of 2015-2018, the number of ASFV-positive cases among wild boar decreased substantially. From the beginning of 2019 to the autumn of 2020, no ASFV-positive wild boar or domestic pigs were detected in Estonia. A new occurrence of ASFV was detected in August 2020, and by the end of 2022, ASFV had been confirmed in seven counties in Estonia. Investigations into proven molecular markers, such as IGR I73R/I329L, MGF505-5R, K145R, O174L, and B602L, were performed with the aim of clarifying whether these cases of ASFV were new entries or remnants of previous epidemics. The sequences from the period of 2014-2022 were compared to the Georgia 2007/1 reference sequence and the variant strains present in Europe. The results indicated that not all the molecular markers of the virus successfully used in other geographical regions were suitable for tracing the spread of ASFV in Estonia. Only the B602L-gene analysis enabled us to place the ASFV isolates spreading in 2020-2022 into two epidemiologically different clusters.

Rapid Identification of ASFV, CSFV and FMDV from Mongolian Outbreaks with MinION Short Amplicon Sequencing

African swine fever virus (ASFV), classical swine fever virus (CSFV), and foot-and-mouth disease virus (FMDV) cause important transboundary animal diseases (TADs) that have a significant economic impact. The rapid and unequivocal identification of these pathogens and distinction from other animal diseases based on clinical symptoms in the field is difficult. Nevertheless, early pathogen detection is critical in limiting their spread and impact as is the availability of a reliable, rapid, and cost-effective diagnostic test. The purpose of this study was to evaluate the feasibility to identify ASFV, CSFV, and FMDV in field samples using next generation sequencing of short PCR products as a point-of-care diagnostic. We isolated nucleic acids from tissue samples of animals in Mongolia that were infected with ASFV (2019), CSFV (2015), or FMDV (2018), and performed conventional (RT-) PCR using primers recommended by the Terrestrial Animal Health Code of the World Organization for Animal Health (WOAH). The (RT-) PCR products were then sequenced in Mongolia using the MinION nanopore portable sequencer. The resulting sequencing reads successfully identified the respective pathogens that exhibited 91-100% nucleic acid similarity to the reference strains. Phylogenetic analyses suggest that the Mongolian virus isolates are closely related to other isolates circulating in the same geographic region. Based on our results, sequencing short fragments derived by conventional (RT-) PCR is a reliable approach for rapid point-of-care diagnostics for ASFV, CSFV, and FMDV even in low-resource countries.

A Guide to Molecular Characterization of Genotype II African Swine Fever Virus: Essential and Alternative Genome Markers

African swine fever is a contagious viral disease that has been spreading through Europe and Asia since its initial report from Georgia in 2007. Due to the large genome size of the causative agent, the African swine fever virus (ASFV), the molecular epidemiology, and virus evolution are analyzed by employing different markers. Most of these markers originate from single nucleotide polymorphisms or disparities in the copy number of tandem repeat sequences observed during the comparisons of full genome sequences produced from ASFVs isolated during different outbreaks. Therefore, consistent complete genome sequencing and comparative analysis of the sequence data are important to add innovative genomic markers that contribute to the delineation of ASFV phylogeny and molecular epidemiology during active circulation in the field. In this study, the molecular markers currently employed to assess the genotype II ASFVs circulating in Europe and Asia have been outlined. The application of each of these markers to differentiate between ASFVs from related outbreaks is described to implement a guideline to their suitability for analyzing new outbreaks. These markers do not signify the complete repertoire of genomic differences between ASFVs, but will be beneficial when analyzing the first outbreaks in a new region or a large number of samples. Furthermore, new markers must be determined via complete genome sequence analyses for enabling in-depth insights into the molecular epidemiology of ASFV.

A multi gene-approach genotyping method identifies 24 genetic clusters within the genotype II-European African swine fever viruses circulating from 2007 to 2022

Introduction

African swine fever (ASF) is a contagious viral disease of pigs and wild boar that poses a major threat to the global swine industry. The genotype II African swine fever virus (ASFV) entered the European Union (EU) in 2014 and since then fourteen countries have been affected, Italy and North Macedonia being the last in 2022. While whole genome sequencing remains the gold standard for the identification of new genetic markers, sequencing of multiple loci with significant variations could be used as a rapid and cost-effective alternative to track outbreaks and study disease evolution in endemic areas.

Materials and methods

To further our understanding of the epidemiology and spread of ASFV in Europe, 382 isolates collected during 2007 to 2022 were sequenced. The study was initially performed by sequencing the central variable region (CVR), the intergenic region (IGR) between the I73R and I329L genes and the O174L and K145R genes. For further discrimination, two new PCRs were designed to amplify the IGR between the 9R and 10R genes of the multigene family 505 (MGF505) and the IGR between the I329L and I215L genes. The sequences obtained were compared with genotype II isolates from Europe and Asia.

Results

The combination of the results obtained by sequencing these variable regions allowed to differentiate the European II-ASFV genotypes into 24 different groups. In addition, the SNP identified in the IGR I329L-I215L region, not previously described, grouped the viruses from North Macedonia that caused the 2022 outbreaks with viruses from Romania, Bulgaria, Serbia and Greece, differentiating from other genotype II isolates present in Europe and Asia. Furthermore, tandem repeat sequence (TRS) within the 9R-10R genes of the multigene family 505 (MGF505) revealed eight different variants circulating.

Discussion

These findings describe a new multi-gene approach sequencing method that can be used in routine genotyping to determine the origin of new introductions in ASF-free areas and track infection dynamics in endemic areas.

Whole-genome sequencing of African swine fever virus from wild boars in the Kaliningrad region reveals unique and distinguishing genomic mutations

Introduction

Since the first report of outbreaks of African swine fever (ASF) in Georgia in 2007, the disease has expanded into Europe, Russia, and Asia, spreading rapidly via contact with infected animals including domestic pigs and wild boars. The vast expansion of this Genotype II African swine fever virus (ASFV) across wide-ranging territories and hosts inevitably led to the acquisition of novel mutations. These mutations could be used to track the molecular epidemiology of ASFV, provided that they are unique to strains restricted within a certain area. Whilst whole-genome sequencing remains the gold standard for examining evolutionary changes, sequencing of a single locus with significant variation and resolution power could be used as a rapid and cost-effective alternative to characterize multiple isolates from a single or related outbreak.

Material and methods

ASFVs obtained during active ASF outbreaks in the Russian region of Kaliningrad between 2017 and 2019 were examined. Since all of the viruses belonged to Genotype II and no clear differentiation based on central variable region (CVR) sequencing was observed, the whole-genome sequences of nine ASFV isolates from this region were determined. To obtain insights into the molecular evolution of these isolates, their sequences were compared to isolates from Europe, Asia, and Africa.

Results

Phylogenetic analysis based on the whole-genome sequences clustered the new isolates as a sister lineage to isolates from Poland and Germany. This suggests a possible shared origin followed by the addition of novel mutations restricted to isolates from this region. This status as a sister lineage was mirrored when analyzing polymorphisms in MGF-505-5R and MGF-110-7L, whilst a polymorphism unique to sequences from Kaliningrad was identified at locus K145R. This newly identified mutation was able to distinguish the isolates obtained from Kaliningrad with sequences of Genotype II ASFVs available on GenBank.

Discussion

The findings of this study suggest that ASFVs circulating in Kaliningrad have recently obtained this mutation providing an additional marker to the mutations previously described.

Experimental Infection of Domestic Pigs with African Swine Fever Virus Isolated in 2019 in Mongolia

African swine fever (ASF) is an infectious viral disease caused by African swine fever virus (ASFV), that causes high mortality in domestic swine and wild boar (Sus scrofa). Currently, outbreaks are mitigated through strict quarantine measures and the culling of affected herds, resulting in massive economic losses to the global pork industry. In 2019, an ASFV outbreak was reported in Mongolia, describing a rapidly progressing clinical disease and gross lesions consistent with the acute form of ASF; the virus was identified as a genotype II virus. Due to the limited information on clinical disease and viral dynamics within hosts available from field observations of the Mongolian isolates, we conducted the present study to further evaluate the progression of clinical disease, virulence, and pathology of an ASFV Mongolia/2019 field isolate (ASFV-MNG19), by experimental infection of domestic pigs. Intramuscular inoculation of domestic pigs with ASFV-MNG19 resulted in clinical signs and viremia at 3 days post challenge (DPC). Clinical disease rapidly progressed, resulting in the humane euthanasia of all pigs by 7 DPC. ASFV-MNG19 infected pigs had viremic titers of 10⁸ TCID₅₀/mL by 5 DPC and shed virus in oral secretions late in disease, as determined from oropharyngeal swabs. Whole-genome sequencing confirmed that the ASFV-MNG19 strain used in this study was a genotype II strain highly similar to other regional strains. In conclusion, we demonstrate that ASFV-MNG19 is a virulent genotype II ASFV strain that causes acute ASF in domestic swine.

Genetic Characterization of African Swine Fever Virus from Pig Farms in South Korea during Outbreaks in 2019-2021

In South Korea, a total of 21 African swine fever (ASF) infected farms were confirmed during 2019-2021. ASF viruses (ASFVs) were isolated from the blood and spleen samples of the 21 affected farms and their genetic characteristics were analyzed. Phylogenetic analysis indicated that the 21 Korean ASFV strains belonged to p72 genotype II and serogroup 8. All isolates were of the intergenic region (IGR) II variant with 10 tandem repeat sequences between I73R and I329L and the central variable region (CVR) 1 variant of the B602L gene. There were no IGR variations between the A179L and A137R and between the MGF 505 9R and10R nor mutations in the O174L, K145R, MGF 505-5R, CP204L, and Bt/Sj regions. The genes of the 21 ASFV strains were identical to those of Georgia 2007/1 and Chinese and Vietnamese strains (Pig/HLJ/2018, China/2018/AnhuiXCGQ, and ASFV_NgheAn_2019); however, X69R of the J268L region of the 18th isolate (Korea/Pig/Goseong/2021) had three nucleotide (CTA) insertions at the 209th position, which led to the addition of one tyrosine (Y) at the C-terminal. This suggests that there are variations among ASFVs circulating in South Korea and the 18th ASFV-infected farm was due to a variant different from those of the other 20 pig farms.

Genetic Characterization of African Swine Fever Virus in Various Outbreaks in Central and Southern Vietnam During 2019-2021

This study aimed to identify potential genetic diversity among African swine fever virus (ASFV) strains circulating in central and southern Vietnam. Thirty ASFV strains were collected from domestic pigs and convalescent pigs with ASFV-infected clinical signs from 19 different provinces of central and southern Vietnam during 2019-2021. A portion of the B646L (p72) gene and the entire E183L (p54), CP204L (p30), and B602L (CVR) genes were amplified, purified, and sequenced. Web-based BLAST and MEGA X software were used for sequence analysis. Analysis of the partial B646L (p72) gene, the full-length E183L (p54) and CP204L (p30) genes, and the central hypervariable region (CVR) of the B602L gene sequence showed that all 30 ASFV isolates belonged to genotype II and were 100% identical to the previously identified strains in Vietnam and China. Analysis of the p72, p54, and p30 regions did not indicate any change in the nucleotide and amino acid sequences among these strains in 3 years of research. No novel variant was found in the CVR within the B602L gene. Analysis of the CVR showed that these ASFV strains belong to subgroup XXXII. The results of this study revealed that these ASFVs shared high similarity with ASFV isolates detected previously in northern Vietnam and China. Taken together, the results of this study and a previous study in Vietnam showed high stability and no genetic diversity in the ASFV genome.

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 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.

Genetic Characterization of the Central Variable Region in African Swine Fever Virus Isolates in the Russian Federation from 2013 to 2017

African swine fever virus (ASFV), classified as genotype II, was introduced into Georgia in 2007, and from there, it spread quickly and extensively across the Caucasus to Russia, Europe and Asia. The molecular epidemiology and evolution of these isolates are predominantly investigated by means of phylogenetic analysis based on complete genome sequences. Since this is a costly and time-consuming endeavor, short genomic regions containing informative polymorphisms are pursued and utilized instead. In this study, sequences of the central variable region (CVR) located within the B602L gene were determined for 55 ASFV isolates submitted from 526 active African swine fever (ASF) outbreaks occurring in 23 different regions across the Russian Federation (RF) between 2013 and 2017. The new sequences were compared to previously published data available from Genbank, representing isolates from Europe and Asia. The sequences clustered into six distinct groups. Isolates from Estonia clustered into groups 3 and 4, whilst sequences from the RF were divided into the remaining four groups. Two of these groups (5 and 6) exclusively contained isolates from the RF, while group 2 included isolates from Russia as well as Chechnya, Georgia, Armenia, Azerbaijan and Ukraine. In contrast, group 1 was the largest, containing sequences from the RF, Europe and Asia, and was represented by the sequence from the first isolate in Georgia in 2007. Based on these results, it is recommended that the CVR sequences contain significant informative polymorphisms to be used as a marker for investigating the epidemiology and spread of genotype II ASFVs circulating in the RF, Europe and Asia.

A systematic review of genotypes and serogroups of African swine fever virus

African swine fever virus (ASFV) is the causative agent of African swine fever (ASF). The virus causes an acute highly hemorrhagic disease in domestic pigs, with high mortality. Although the overall genome mutation rate of ASFV, a large DNA virus, is relatively low, ASFV exhibits genetic and antigenic diversity. ASFV can be classified into 24 genotypes on the basis of the B646L gene. Cross-protected ASFV strains can be divided into eight serogroups on the basis of antibody-mediated hemadsorption inhibition. Here, we review research progress on ASFV genotyping and serogrouping, and explain how this information assists in the rapid identification of virus origin during ASF outbreaks and will aid in the development of ASF vaccines.

African Swine Fever in Wild Boar (Poland 2020): Passive and Active Surveillance Analysis and Further Perspectives

African swine fever (ASF) is a fatal hemorrhagic disease of wild boar and domestic pigs which has been present in Poland since 2014. By 2020, the ASF virus (ASFV) spread across Central, Eastern and Western Europe (including Germany), and Asian countries (including China, Vietnam, and South Korea). The national ASF eradication and prevention program includes continuous passive (wild boar found dead and road-killed wild boar) and active (hunted wild boar) surveillance. The main goal of this study was to analyze the dynamic of the spread of ASF in the wild boar population across the territory of Poland in 2020. In that year in Poland, in total 6191 ASF-positive wild boar were declared. Most of them were confirmed in a group of animals found dead. The conducted statistical analysis indicates that the highest chance of obtaining an ASF-positive result in wild boar was during the winter months, from January to March, and in December 2020. Despite the biosecurity measures implemented by holdings of domestic pigs, the disease also occurred in 109 pig farms. The role of ASF surveillance in the wild boar population is crucial to apply more effective and tailored measures of disease control and eradication. The most essential measures to maintain sustainable production of domestic pigs in Poland include effective management of the wild boar population, along with strict implementation of biosecurity measures by domestic pig producers.

Dynamics of African swine fever virus (ASFV) infection in domestic pigs infected with virulent, moderate virulent and attenuated genotype II ASFV European isolates

This study aimed to compare the infection dynamics of three genotype II African swine fever viruses (ASFV) circulating in Europe. Eighteen domestic pigs divided into three groups were infected intramuscularly or by direct contact with two haemadsorbent ASFVs (HAD) from Poland (Pol16/DP/ OUT21) and Estonia (Est16/WB/Viru8), and with the Latvian non-HAD ASFV (Lv17/WB/Rie1). Parameters, such as symptoms, pathogenicity, and distribution of the virus in tissues, humoral immune response, and dissemination of the virus by blood, oropharyngeal and rectal routes, were investigated. The Polish ASFV caused a case of rapidly developing fatal acute disease, while the Estonian ASFV caused acute to sub-acute infections and two animals survived. In contrast, animals infected with the ASFV from Latvia developed a more subtle, mild, or even subclinical disease. Oral excretion was sporadic or even absent in the attenuated group, whereas in animals that developed an acute or sub-acute form of ASF, oral excretion began at the same time the ASFV was detected in the blood, or even 3 days earlier, and persisted up to 22 days. Regardless of virulence, blood was the main route of transmission of ASFV and infectious virus was isolated from persistently infected animals for at least 19 days in the attenuated group and up to 44 days in the group of moderate virulence. Rectal excretion was limited to the acute phase of infection. In terms of diagnostics, the ASFV genome was detected in contact pigs from oropharyngeal samples earlier than in blood, independently of virulence. Together with blood, both samples could allow to detect ASFV infection for a longer period. The results presented here provide quantitative data on the spread and excretion of ASFV strains of different virulence among domestic pigs that can help to better focus surveillance activities and, thus, increase the ability to detect ASF introductions earlier.

Demand-driven spreading patterns of African swine fever in China

African swine fever (ASF) is a highly contagious hemorrhagic viral disease of domestic and wild pigs. ASF has led to major economic losses and adverse impacts on livelihoods of stakeholders involved in the pork food system in many European and Asian countries. While the epidemiology of ASF virus (ASFV) is fairly well understood, there is neither any effective treatment nor vaccine. In this paper, we propose a novel method to model the spread of ASFV in China by integrating the data of pork import/export, transportation networks, and pork distribution centers. We first empirically analyze the overall spatiotemporal patterns of ASFV spread and conduct extensive experiments to evaluate the efficacy of a number of geographic distance measures. These empirical analyses of ASFV spread within China indicate that the first occurrence of ASFV has not been purely dependent on the geographical distance from existing infected regions. Instead, the pork supply-demand patterns have played an important role. Predictions based on a new distance measure achieve better performance in predicting ASFV spread among Chinese provinces and thus have the potential to enable the design of more effective control interventions.

Comparative Analysis of Full Genome Sequences of African Swine Fever Virus Isolates Taken from Wild Boars in Russia in 2019

In this study, we report on the full genome phylogenetic analysis of four ASFV isolates obtained from wild boars in Russia. These samples originated from two eastern and two western regions of Russia in 2019. Phylogenetic analysis indicated that the isolates were assigned to genotype II and grouped according to their geographical origins. The two eastern isolates shared 99.99% sequence identity with isolates from China, Poland, Belgium, and Moldova, whereas the western isolates had 99.98% sequence identity with isolates from Lithuania and the original Georgia 2007 isolate. Based on the full genome phylogenies, we identified three single locus targets, MGF-360-10L, MGF-505-9R, and I267L, that yielded the same resolving power as the full genomes. The ease of alignment and a high level of variation make these targets a suitable selection as additional molecular markers in future ASFV phylogenetic practices.

ASF Exit Strategy: Providing cumulative evidence of the absence of African swine fever virus circulation in wild boar populations using standard surveillance measures

EFSA assessed the role of seropositive wild boar in African swine fever (ASF) persistence. Surveillance data from Estonia and Latvia investigated with a generalised equation method demonstrated a significantly slower decline in seroprevalence in adult animals compared with subadults. The seroprevalence in adults, taking more than 24 months to approach zero after the last detection of ASFV circulation, would be a poor indicator to demonstrate the absence of virus circulation. A narrative literature review updated the knowledge on the mortality rate, the duration of protective immunity and maternal antibodies and transmission parameters. In addition, parameters potentially leading to prolonged virus circulation (persistence) in wild boar populations were reviewed. A stochastic explicit model was used to evaluate the dynamics of virus prevalence, seroprevalence and the number of carcasses attributed to ASF. Secondly, the impact of four scenarios on the duration of ASF virus (ASFV) persistence was evaluated with the model, namely a: (1) prolonged, lifelong infectious period, (2) reduction in the case-fatality rate and prolonged transient infectiousness; (3) change in duration of protective immunity and (4) change in the duration of protection from maternal antibodies. Only the lifelong infectious period scenario had an important prolonging effect on the persistence of ASF. Finally, the model tested the performance of different proposed surveillance strategies to provide evidence of the absence of virus circulation (Exit Strategy). A two-phase approach (Screening Phase, Confirmation Phase) was suggested for the Exit Strategy. The accuracy of the Exit Strategy increases with increasing numbers of carcasses collected and tested. The inclusion of active surveillance based on hunting has limited impact on the performance of the Exit Strategy compared with lengthening of the monitoring period. This performance improvement should be reasonably balanced against an unnecessary prolonged 'time free' with only a marginal gain in performance. Recommendations are provided for minimum monitoring periods leading to minimal failure rates of the Exit Strategy. The proposed Exit Strategy would fail with the presence of lifelong infectious wild boar. That said, it should be emphasised that the existence of such animals is speculative, based on current knowledge.

Genetic Analysis of African Swine Fever Virus From the 2018 Outbreak in South-Eastern Burundi

African swine fever (ASF) is a contagious viral disease that causes high mortality, approaching 100%, in domestic pigs and wild boars. The disease has neither a cure nor a vaccine, and it is caused by an ASF virus (ASFV), the only member of the family Asfarviridae, genus Asfivirus, and the only known DNA arbovirus. Twenty-four genotypes of ASFV have been described to date, and all of them have been described in Africa. ASF is endemic in Burundi, and several outbreaks have been reported in the country; the disease continues to economically impact on small-scale farmers. This study aimed at genetic characterization of ASFV that caused an ASF outbreak in the Rutana region, Burundi, in the year 2018. Tissue samples from domestic pigs that died as a result of a severe hemorrhagic disease were collected in order to confirm the disease using polymerase chain reaction (PCR) and to conduct partial genome sequencing. Nucleotide sequences were obtained for the B646L (p72) gene, the intergenic fragment between the I73R and I329L genes, and the central variable region (CVR) of the B602L gene. Phylogenetic analysis of the Burundian 2018 ASFV grouped the virus within B646L (p72) genotype X and clustered together with those reported during the 1984 and 1990 outbreaks in Burundi with high nucleotide identity to some ASFV strains previously reported in neighboring East African countries, indicating a regional distribution of this ASFV genotype. Analysis of the intergenic fragment between I73R and I329L genes showed that the Burundian 2018 ASFV described in this study lacked a 32–base pair (bp) fragment present in the reference genotype X strain, Kenya 1950. In addition, the strain described in this study had the signature AAABNAABA at the CVR (B602L) gene and showed 100% amino acid sequence identity to viruses responsible for recent ASF outbreaks in the region. The virus described in this study showed high genetic similarities with ASFV strains previously described in domestic pigs, wild suids, and soft ticks in East African countries, indicating a possible common wild source and continuous circulation in domestic pigs in the region.

Isolation and Genetic Characterization of African Swine Fever Virus from Domestic Pig Farms in South Korea, 2019

On 17 September 2019, the first outbreak of African swine fever in a pig farm was confirmed in South Korea. By 9 October, 14 outbreaks of ASF in domestic pigs had been diagnosed in 4 cities/counties. We isolated viruses from all infected farms and performed genetic characterization. The phylogenetic analysis showed that all of fourteen ASFV isolates in South Korea belong to genotype II and serogroup 8. Additionally, all isolates had an intergenic region (IGR) II variant with additional tandem repeat sequences (TRSs) between the I73R and I329L genes and showed characteristics of central variable region (CVR) 1 of the B602L gene and IGR 1 of MGF 505 9R/10R genes. These are identical to the genetic characteristics of some European isolates and Chinese isolates.

The Spillover of African Swine Fever in Western Poland Revealed Its Estimated Origin on the Basis of O174L, K145R, MGF 505-5R and IGR I73R/I329L Genomic Sequences

The African swine fever epidemic occurred in Poland at the beginning of 2014 and, up to date, the disease has been spreading mainly in the eastern part of the country. Unexpectedly, in November 2019 an infected wild boar case was confirmed in Lubuskie voivodship in western Poland. During the following weeks, several dozen African swine fever virus (ASFV)-positive animals were notified in the neighboring area, causing severe concern regarding further spread of the disease to the mostly pig-dense region in Poland, namely, Wielkopolskie voivodship. Moreover, almost a year after, several infected wild boar cases were confirmed for the first time in Germany, just beyond the Polish border, sending out a shock wave through the global pig market. The whole genome sequence of ASFV, isolated from the first case of ASF in western Poland, and three selected viruses from other affected areas, revealed the tandem repeat and single nucleotide polymorphism (SNP) variations in reference to the Georgia 2007/1 strain. These data, supported by the conventional sequencing of selected genomic regions from a total of 154 virus samples isolated between 2017 and 2020 in Poland, shed a new light on pathogen epidemiology. The sequence variations within the O174L gene detected in this study showed that cases identified in western Poland might be originating from the so-called southern Warsaw cluster. Moreover, the viruses originating from the northern Warsaw cluster do not possess single nucleotide polymorphism (SNP) mutations within the K145R and MGF 505-5R genes, which are specific to all of the other Polish ASFV strains. These results led to a conclusion of their distinct origin. Supporting these results, the nucleotide sequencing of I73R/I329L intergenic region revealed its new, previously undescribed variant, called IGR IV, with an additional three tandem repeats of 10 nucleotides in comparison to the reference sequence of the Georgia 2007/1 strain.