Review of the Pig-Adapted African Swine Fever Viruses in and Outside Africa

A triplex crystal digital PCR for the detection of genotypes I and II African swine fever virus

African swine fever (ASF) is a highly contagious and lethal viral disease that causes severe hemorrhagic fever in pigs. It keeps spreading around the world, posing a severe socioeconomic risk and endangering biodiversity and domestic food security. ASF first outbroke in China in 2018, and has spread to most provinces nationwide. Genotypes I and II ASF virus (ASFV) as the etiological pathogens have been found in China. In this study, three pairs of specific primers and probes targeting the ASFV B646L gene, F1055L gene, and E183L gene were designed to detect universal, genotype I, and genotype II strains, respectively. A triplex crystal digital PCR (cdPCR) was established on the basis of optimizing various reaction conditions. The assay demonstrated remarkably sensitive with low limits of detection (LODs) of 5.120, 4.218, 4.588 copies/reaction for B646L, F1055L, and E183L gene, respectively; excellent repeatability with 1.24-2.01% intra-assay coefficients of variation (CVs) and 1.32-2.53% inter-assay CVs; good specificity for only detection of genotypes I and II ASFV, without cross-reactivity with PCV2, PRV, SIV, PRRSV, PEDV, FMDV, and CSFV. The triplex cdPCR was used to test 1,275 clinical samples from Guangxi province of China, and the positivity rates were 5.05, 3.22, and 1.02% for genotype I, genotype II, and co-infection of genotypes I and II, respectively. These 1,275 clinical samples were also detected using a reported reference triplex real-time quantitative PCR (qPCR), and the agreements of detection results between these two methods were more than 98.98%. In conclusion, the developed triplex cdPCR could be used as a rapid, sensitive, and accurate method to detect and differentiate genotypes I and II strains of ASFV.

Detection of antibodies against Ornithodoros moubata salivary antigens and their association with detection of African swine fever virus in pigs slaughtered in central Uganda

Introduction

African swine fever (ASF) is an important disease of pigs in sub-Saharan Africa and Uganda and is threatening the pig population and agricultural economy of other continents. ASF virus (ASFV) can be transmitted from wild suids to domestic pigs through soft ticks of the Ornithodoros species. The aim of this study was to understand the relationship between domestic pigs' O. moubata tick exposure and ASFV status.

Methods

Pigs were sampled from six abattoirs in the Kampala metropolitan area of Uganda from May 2021 through June 2022. Blood, serum, and tissue samples were collected. Serum was tested for antibodies against the rtTSGP1 salivary antigens of O. moubata ticks using an indirect ELISA assay. Blood and tissue samples from pigs were tested to detect ASFV using qPCR. Probability of tick exposure was categorized based on sample-to-positive ratio cut-off points.

Results

Out of 1,328 serum samples tested, there were 828 (62.3%) samples with a negligible probability; 369 (27.8%) with a medium probability; 90 (6.8%) with a high probability, and 41 (3.1%) with a very high probability of exposure to the O. moubata salivary antigen. There was a statistically significant association between the pigs' O. moubata exposure and ASFV status with a higher proportion of pigs having a very high probability of infection if they were ASFV positive by blood, tonsil, and lymph nodes.

Discussion

These results suggested that tick exposure was associated with ASFV transmission in Uganda. There were ASFV qPCR positive pigs that had no O. moubata exposure as well, which highlights that pig-to-pig and indirect contact transmission still play a significant role. This work highlights the need for further work in Uganda to investigate these transmission factors related to the O. moubata tick and ASFV transmission.

Passive Surveillance as a Key Tool for African Swine Fever Eradication in Wild Boar: A Protocol to Find Carcasses Tested and Validated in the Mediterranean Island of Sardinia

African swine fever (ASF) is one of the most important and serious contagious hemorrhagic viral diseases affecting domestic pigs and wild boar and is associated with high mortality rates while also having an extensive sanitary and socioeconomic impact on the international trade of animal and swine products. The early detection of the disease is often hampered by inadequate surveillance. Among the surveillance strategies used, passive surveillance of wild boars is considered the most effective method for controlling the African swine fever virus (ASFV). Otherwise, the design of a sufficiently sensitive ASF surveillance system requires a solid understanding of the epidemiology related to the local eco-social context, especially in the absence of virus detection. Even if the number of carcasses needed to demonstrate ASF eradication has been established, the scientific context lacks detail compared to protocols applied in the active search for wild boar carcasses. The aim of this study was to describe the protocol applied in the active search for carcasses, providing detailed information on the number of people and dogs as well as the amount of time and space used within the Mediterranean area. Using a specific tool developed to record, trace, and share field data (the GAIA observer app), a total of 33 active searches for wild boar carcasses were organized during 2021-2023. Most of these searches were planned to find carcasses that had previously been reported by hunters. A total of 24 carcasses were found, with only 2 carcasses not previously reported. The final protocol applied involved four people, with an average speed of 1.5 km/h. When a carcass had been previously reported, about 2 km of distance had to be covered in about 1.5 h to find the carcass, and even less time was spent when a dog (untrained) was present. In conclusion, it can be stated that, when searching for carcasses, solid collaboration with local hunters or other forest visitors is necessary to ensure carcasses are reported. The process involves small groups of experts actively searching for carcasses, possibly with the use of hunting dogs without special training. The data presented could be of valid support for those countries characterized by Mediterranean vegetation that are faced with the need to plan active carcass searches.

Development of a triplex real-time quantitative PCR for detection and differentiation of genotypes I and II African swine fever virus

African swine fever virus (ASFV) was first identified in 1921 and is extensively prevalent around the world nowadays, which has a significant negative impact on the swine industry. In China, genotype II ASFV was first discovered in 2018, and has spread quickly to different provinces in a very short time; genotype I ASFV was first found in 2020, and has been reported in several provinces since then. To establish an accurate method for detection and differentiation of genotypes I and II ASFV, three primers and probes were designed targeting the ASFV B646L gene for different genotypes, the F1055L gene for genotype I, and the E183L gene for genotype II, and a triplex real-time quantitative PCR (qPCR) for differential detection of genotypes I and II ASFV was developed after optimizing the reaction conditions. The assay showed high sensitivity, and the limits of detection (LOD) of the B646L, F1055L, and E183L genes were 399.647 copies/reaction, 374.409 copies/reaction, and 355.083 copies/reaction, respectively; the coefficients of variation (CVs) of the intra-assay and the inter-assay were 0.22-1.88% and 0.16-1.68%, respectively, showing that this method had good repeatability; the assay could detect only ASFV, without cross-reactivity with other swine viruses including PRRSV, PEDV, PDCoV, CSFV, PRV, and PCV2, showing excellent specificity of this method. A total of 3,519 clinical samples from Guangxi province, southern China, were tested by the developed assay, and 8.16% (287/3,519) samples were found to be positive for ASFV, of which 0.17% (6/3,519) samples were positive for genotype I, 7.19% (253/3,519) samples for genotype II, and 0.80% (28/3,519) samples for genotypes I and II. At the same time, these clinical samples were also tested by a previously reported multiplex qPCR, and the agreement between these two methods was more than 99.94%. In summary, the developed triplex qPCR provided a fast, specific and accurate method for detection and differentiation of genotypes I and II ASFV.

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

Since 2018, the outbreaks of genotype II African swine fever virus (ASFV) in China and several eastern Asian countries have 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 3 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 strains 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.

Triplex Crystal Digital PCR for the Detection and Differentiation of the Wild-Type Strain and the MGF505-2R and I177L Gene-Deleted Strain of African Swine Fever Virus

African swine fever (ASF) is a severe and highly contagious viral disease that affects domestic pigs and wild boars, characterized by a high fever and internal bleeding. The disease is caused by African swine fever virus (ASFV), which is prevalent worldwide and has led to significant economic losses in the global pig industry. In this study, three pairs of specific primers and TaqMan probes were designed for the ASFV B646L, MGF505-2R and I177L genes. After optimizing the reaction conditions of the annealing temperature, primer concentration and probe concentration, triplex crystal digital PCR (cdPCR) and triplex real-time quantitative PCR (qPCR) were developed for the detection and differentiation of the wild-type ASFV strain and the MGF505-2R and/or I177L gene-deleted ASFV strains. The results indicate that both triplex cdPCR and triplex qPCR were highly specific, sensitive and repeatable. The assays could detect only the B646L, MGF505-2R and I177L genes, without cross-reaction with other swine viruses (i.e., PRRSV, CSFV, PCV2, PCV3, PEDV, PDCoV and PRV). The limit of detection (LOD) of triplex cdPCR was 12 copies/reaction, and the LOD of triplex qPCR was 500 copies/reaction. The intra-assay and inter-assay coefficients of variation (CVs) for repeatability and reproducibility were less than 2.7% for triplex cdPCR and less than 1.8% for triplex qPCR. A total of 1510 clinical tissue samples were tested with both methods, and the positivity rates of ASFV were 14.17% (214/1510) with triplex cdPCR and 12.98% (196/1510) with triplex qPCR, with a coincidence rate of 98.81% between the two methods. The positivity rate for the MGF505-2R gene-deleted ASFV strains was 0.33% (5/1510), and no I177L gene-deleted ASFV strain was found. The results indicate that triplex cdPCR and triplex qPCR developed in this study can provide rapid, sensitive and accurate methods for the detection and differentiation of the ASFV B646L, MGF505-2R and I177L genes.

African Swine Fever: Epidemiology, the Design of New Diagnostic Methods, and Vaccine Development

African swine fever (ASF) is a pandemic viral disease that poses a major threat to the health of wild and domestic pigs, national economies, and subsistence livelihoods around the world [...].

The live pig supply chain as reported by farmers in selected districts affected by African swine fever in Uganda, June and July 2022

Introduction

Uganda is a pork-producing country in East Africa. The African swine fever virus (ASFV) has had a devastating impact on the country's pig industry. The movements of pigs and pork are a major pathway of spreading ASFV. This study was done to describe the live pig supply chain within and through districts that are impacted by African swine fever (ASF) in Uganda.

Methods

A pig farmer survey in districts known to have ASFV was done using a semi-structured questionnaire available in English and two local languages. In total, 99 farmers were interviewed across five districts. Farmers were conveniently and purposively selected by local government veterinary officials. An online key informant survey was also used to validate farmer responses.

Results

Most farmers interviewed in all districts reported to source and sell most of their pigs from within their district the farm was in, although there was variation by district and pig type. In relation to pig type, 89.7% of farmers sourced sows, 80.0% sourced boars, and 96.4% sourced weaned pigs from the district where the farm was located. As for sales, 91.3% of farmers sold sows, 92.7% sold boars, 91.9% sold weaned pigs, and 92.2% sold market pigs in the district where the farm was located. There was also variation to whom pigs were sold and sourced by pig type.

Conclusion

This information is useful when planning the scale and focus of disease control programs based on animal movement. This study revealed that pig disease control programs can be targeted to smaller regions. Furthermore, there is a need for farmers and pig traders to be educated on and adhere to veterinary regulations of animal movement and good biosecurity practices to reduce disease spread when purchasing and selling pigs from known ASFV infected areas.

An Updated Review of Ornithodoros Ticks as Reservoirs of African Swine Fever in Sub-Saharan Africa and Madagascar

This updated review provides an overview of the available information on Ornithodoros ticks as reservoirs and biological vectors of the ASF virus in Africa and Indian Ocean islands in order to update the current knowledge in this field, inclusive of an overview of available methods to investigate the presence of ticks in the natural environment and in domestic pig premises. In addition, it highlights the major areas of research that require attention in order to guide future investigations and fill knowledge gaps. The available information suggests that current knowledge is clearly insufficient to develop risk-based control and prevention strategies, which should be based on a sound understanding of genotype distribution and the potential for spillover from the source population. Studies on tick biology in the natural and domestic cycle, including genetics and systematics, represent another important knowledge gap. Considering the rapidly changing dynamics affecting the African continent (demographic growth, agricultural expansion, habitat transformation), anthropogenic factors influencing tick population distribution and ASF virus (ASFV) evolution in Africa are anticipated and have been recorded in southern Africa. This dynamic context, together with the current global trends of ASFV dissemination, highlights the need to prioritize further investigation on the acarological aspects linked with ASF ecology and evolution.

Effects of Disinfectants on Larval Growth and Gut Microbial Communities of Black Soldier Fly Larvae

The use of the black soldier fly has been demonstrated to be effective in the treatment of swine manure. Since the outbreaks of ASFV, prevention procedures, including manure disinfection, have changed dramatically. Glutaraldehyde (GA) and potassium peroxymonosulfate (PPMS) have been shown to be effective in the prevention of this pathogen and are thus widely used in the disinfection of swine manures, etc. However, research on the effects of disinfectants in manures on the growth of BSFL and gut microbiota is scarce. The goal of this study was to determine the effects of GA and PPMS on BSFL growth, manure reduction, and gut microbiota. In triplicate, 100 larvae were inoculated in 100 g of each type of manure compound (manure containing 1% GA treatment (GT1), manure containing 0.5% GA treatment (GT2), manure containing 1% PPMS treatment (PT1), manure containing 0.5% PPMS treatment (PT2), and manure without disinfectant (control)). After calculating the larval weight and waste reduction, the larval gut was extracted and used to determine the microbial composition. According to the results, the dry weights of the larvae fed PT1-2 (PT1: 86.7 ± 4.2 mg and PT2: 85.3 ± 1.3 mg) were significantly higher than those of the larvae fed GT1-2 (GT1: 72.5 ± 2.1 mg and GT2: 70 ± 2.8 mg) and the control (64.2 ± 5.8 mg). There was a 2.8-4.03% higher waste reduction in PT1-2 than in the control, and the waste reduction in GT1-2 was 7.17-7.87% lower than that in the control. In a gut microbiota analysis, two new genera (Fluviicola and Fusobacterium) were discovered in PT1-2 when compared to GT1-2 and the control. Furthermore, the disinfectants did not reduce the diversity of the microbial community; rather, Shannon indices revealed that the diversities of GT1-2 (GT1: 1.924 ± 0.015; GT2: 1.944 ± 0.016) and PT1 (1.861 ± 0.016) were higher than those of the control (1.738 ± 0.015). Finally, it was found that both disinfectants in swine manures at concentrations of 1% and 0.5% may be beneficial to the complexity and cooperation of BSFL gut microbiota, according to an analysis of microbial interactions.