Molecular characterization of African swine fever virus from outbreaks in Namibia in 2018

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

The region in eastern, central and southern Africa (ECSA) where African swine fever (ASF) originated in a sylvatic cycle is home to all the p72 genotypes of ASF virus identified so far. While 20 of the 24 genotypes have been isolated from outbreaks in domestic pigs in the region, only five of the genotypes (I, II, VIII, IX, X) have an extended field presence associated with domestic pigs. Of the genotypes that appear to be strongly adapted to domestic pigs, two have spread beyond the African continent and have been the focus of efforts to develop vaccines against ASF. Most of the experimental ASF vaccines described do not protect against a wider spectrum of viruses and may be less useful in the event of incursions of different strains or where multiple genotypes co-exist. The other three pig-adapted strains that are currently restricted to the ECSA region might spread, and priority should be given to understanding not only the genetic and antigenic characteristics of these viruses but also their history. We review historic and current knowledge of the distribution of these five virus genotypes, and note that as was the case for genotype II, some pig-associated viruses have the propensity for geographical range expansion. These features are valuable for prioritizing vaccine-development efforts to ensure a swift response to virus escape. However, whilst ASF vaccines are critical for high-production systems, global food security relies on parallel efforts to improve biosecurity and pig production in Africa and on continued ASFV surveillance and characterisation in the ECSA region.

Detection of African Swine Fever Virus in Ornithodoros Tick Species Associated with Indigenous and Extralimital Warthog Populations in South Africa

We investigated the possibility that sylvatic circulation of African swine fever virus (ASFV) in warthogs and Ornithodoros ticks had extended beyond the historically affected northern part of South Africa that was declared a controlled area in 1935 to prevent the spread of infection to the rest of the country. We recently reported finding antibody to the virus in extralimital warthogs in the south of the country, and now describe the detection of infected ticks outside the controlled area. A total of 5078 ticks was collected at 45 locations in 7/9 provinces during 2019-2021 and assayed as 711 pools for virus content by qPCR, while 221 pools were also analysed for tick phylogenetics. Viral nucleic acid was detected in 50 tick pools representing all four members of the Ornithodoros (Ornithodoros) moubata complex known to occur in South Africa: O. (O.) waterbergensis and O. (O.) phacochoerus species yielded ASFV genotypes XX, XXI, XXII at 4 locations and O. (O.) moubata yielded ASFV genotype I at two locations inside the controlled area. Outside the controlled area, O. (O.) moubata and O. (O.) compactus ticks yielded ASFV genotype I at 7 locations, while genotype III ASFV was identified in O. (O.) compactus ticks at a single location. Two of the three species of the O. (O.) savignyi complex ticks known to be present in the country, O. (O.) kalahariensis and O. (O.) noorsveldensis, were collected at single locations and found negative for virus. The only member of the Pavlovskyella subgenus of Ornithodoros ticks known to occur in South Africa, O. (P.) zumpti, was collected from warthog burrows for the first time, in Addo National Park in the Eastern Cape Province where ASFV had never been recorded, and it tested negative for the viral nucleic acid. While it is confirmed that there is sylvatic circulation of ASFV outside the controlled area in South Africa, there is a need for more extensive surveillance and for vector competence studies with various species of Ornithodoros ticks.

Viral Co-Infections of Warthogs in Namibia with African Swine Fever Virus and Porcine Parvovirus 1

Simple Summary

Wild animals can transmit diseases to domestic animals. In Africa, warthogs are known to be carriers of pathogens that can infect pigs; consequently, it is important to identify these pathogens in order to protect pigs from infection. In this study, two important swine pathogens i.e., African swine fever virus (ASFV) and porcine parvovirus 1 (PPV1) were identified in warthogs in Namibia and characterized genetically. The results will be of interest to those working in swine disease management and control in Namibia.

Abstract

Understanding virus circulation in wild animals, particularly those that have contact with domestic animals, is crucial for disease management and control. In Africa, warthogs are known to be asymptomatic carriers of porcine pathogens; a recent study in Namibia has shown them to be positive for Porcine circovirus-2 (PCV-2). In this study, the same samples used for the PCV-2 investigation in Namibia were further screened for the presence of African swine fever virus (ASFV) and porcine parvovirus 1 (PPV1) by PCR. Of the 42 animals tested, 2 (4.8%) and 13 (31%) were positive for AFSV and PPV1, respectively. The two AFSV were also co-infected with PPV1. Combing the results of this study with the results of the previous PCV-2 investigation, four warthogs were shown to be co-infected with both PPV1 and PCV-2. Sequence and phylogenetic analysis revealed that the AFSV belonged to genotype (Ib) but were from different serogroups. Unexpectedly, the ASFVs from the warthogs were genetically distinct to those observed in an outbreak in the same region of Namibia that occurred less than fifteen months prior to the sampling of the warthogs. In fact, a stronger genetic relationship was observed between the warthog viruses and historical Namibian and South African ASFVs identified in 1980, 2004 and 2008. For the PPV1s, the closest relative to the Namibian PPV1 were viruses identified in wild boar in Romania in 2011. This study confirms that warthogs are carriers of porcine pathogens and the data should encourage further studies on larger populations of wild and domestic swine to more fully understand the epidemiology and transmission of viral pathogens from these species.

Molecular Characterization of African Swine Fever Virus From 2019-2020 Outbreaks in Guangxi Province, Southern China

African swine fever virus (ASFV) causes contagious hemorrhagic disease of pigs with high morbidity and mortality. To identify the molecular characteristics of ASFV strains circulating in Guangxi province, southern China, a total of 336 tissue samples collected from 336 domestic pigs that died as a result of severe hemorrhagic disease during 2019–2020 were tested for ASFV. Furthermore, 66 ASFV strains were genetically characterized by sequence analysis of the C-terminal region of B646L (p72) gene, the complete E183L (p54) gene, the variable region of EP402R (CD2v) gene, the central variable region (CVR) of B602L gene, the full MGF505-2R gene, and the tandem repeat sequence (TRS) within intergenic region (IGR) between the I73R and I329L (I73R/I329L) genes. Phylogenetic analysis revealed that the ASFV strains from Guangxi province belonged to genotypes I and II based on the B646L (p72) and E183L (p54) genes, and there were eight different tetrameric TRS variants based on the CVR of B602L gene. Phylogenetic analysis of the EP402R (CD2v) gene revealed that these ASFV strains belonged to serogroups 4 and 8. Eight of the 66 strains belonged to genotype I and serogroup 4, and showed deletion of whole MGF505-2R gene. The sequence analysis of the IGR between the I73R/I329L genes showed that IGR II and III variants were co-circulating in Guangxi province. The results indicated that ASFV strains circulating in Guangxi province during 2019–2020 outbreaks showed high genetic diversity, of which genotypes I and II, as well as serogroups 4 and 8, were simultaneously circulating in Guangxi province, and there existed wild-type and naturally gene-deleted strains in the field. This is the first detailed report on the molecular characterization of the ASFV strains circulating in southern China, and serogroup 4 in China.

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

The evolutionary and demographic history of African swine fever virus (ASFV) is potentially quite valuable for developing efficient and sustainable management strategies. In this study, we performed phylogenetic, phylodynamic, and phylogeographic analyses of worldwide ASFV based on complete ASFV genomes, B646L gene, and E183L gene sequences obtained from NCBI to understand the epidemiology of ASFV. Bayesian phylodynamic analysis and phylogenetic analysis showed highly similar results of group clustering between E183L and the complete genome. The evidence of migration and the demographic history of ASFV were also revealed by the Bayesian phylodynamic analysis. The evolutionary rate was estimated to be 1.14 × 10⁻⁵ substitution/site/year. The large out-migration from the viral population in South Africa played a crucial role in spreading the virus worldwide. Our study not only provides resources for the better utilization of genomic data but also reveals the comprehensive worldwide evolutionary history of ASFV with a broad sampling window across ~70 years. The characteristics of the virus spatiotemporal transmission are also elucidated, which could be of great importance for devising strategies to control the virus.

Functional Analysis and Proteomics Profiling of Extracellular Vesicles From Swine Plasma Infected by African Swine Fever Virus

African swine fever (ASF) has brought excellent barriers to swine production in China and the world. Studies have shown that extracellular vesicles mediate the RNA and protein spread of pathogenic microorganisms and RNA and proteins. After infection by pathogenic microorganisms causes significant differences in the proteins contained within extracellular vesicles. Based on the above studies, the extracellular vesicles were extracted from ASF virus (ASFV)-infected swine plasma. And qPCR, western blot, and confocal experiment were carried out. The research shows that extracted extracellular vesicles significantly promote the replication of ASFV in susceptible and non-susceptible cells Proteomics analysis of the extracellular vesicle proteins revealed that ASFV infection could cause significant differences in the protein profile. This study demonstrates that extracellular vesicles play a critical role in ASFV replication and transmission and cause significant differences in the protein profile encapsulated in extracellular vesicles.

One hundred years of African swine fever in Africa: where have we been, where are we now, where are we going?

One hundred years have passed since the first paper on African swine fever (ASF) was published by Montgomery in 1921. With no vaccine, ineffectiveness of prevention and control measures, and lack of common interest in eradicating the disease, ASF has proven to be one of the most devastating diseases because of its significant sanitary and socioeconomic consequences. The rapid spread of the disease on the European and Asian continents and its recent appearance in the Caribbean puts all countries at great risk because of global trade. The incidence of ASF has also increased on the African continent over the last few decades, extending its distribution far beyond the area in which the ancient sylvatic cycle is present with its complex epidemiological transmission pathways involving virus reservoirs in ticks and wild African Suidae. Both in that area and elsewhere, efficient transmission by infected domestic pigs and virus resistance in infected animal products and fomites mean that human driven factors along the pig value chain are the dominant impediments for its prevention, control, and eradication. Control efforts in Africa are furthermore hampered by the lack of information about the size and location of the fast-growing pig population, particularly in the dynamic smallholder sector that constitutes up to 90% of pig production in the region. A vaccine that will be both affordable and effective against multiple genotypes of the virus is not a short-term reality. Therefore, a strategy for management of ASF in sub-Saharan Africa is needed to provide a roadmap for the way forward for the continent. This review explores the progression of ASF and our knowledge of it through research over a century in Africa, our current understanding of ASF, and what must be done going forwards to improve the African situation and contribute to global prevention and control. This article is protected by copyright. All rights reserved.

African Swine Fever Virus (ASFV): Biology, Genomics and Genotypes Circulating in Sub-Saharan Africa

African swine fever (ASF) is a highly infectious and fatal haemorrhagic disease of pigs that is caused by a complex DNA virus of the genus Asfivirus and Asfarviridae African suids family. The disease is among the most devastating pig diseases worldwide including Africa. Although the disease was first reported in the 19th century, it has continued to spread in Africa and other parts of the world. Globally, the rising demand for pork and concomitant increase in transboundary movements of pigs and pork products is likely to increase the risk of transmission and spread of ASF and pose a major challenge to the pig industry. Different genotypes of the ASF virus (ASFV) with varying virulence have been associated with different outbreaks in several countries in sub-Saharan Africa (SSA) and worldwide, and understanding genotype circulation will be important for ASF prevention and control strategies. ASFV genotypes unique to Africa have also been reported in SSA. This review briefly recounts the biology, genomics and genotyping of ASFV and provides an account of the different genotypes circulating in SSA. The review also highlights prevention, control and progress on vaccine development and identifies gaps in knowledge of ASFV genotype circulation in SSA that need to be addressed.

Synergistic effect of the responses of different tissues against African swine fever virus

African swine fever is an acute, haemorrhagic fever and contagious disease of pigs caused by African swine fever virus (ASFV), which has a great impact on the pig farming industry and related international trade. Understanding the response processes of various tissues in pigs after ASFV infection may help to address current major concerns, such as the exploration of key genes for vaccine development, the cooperative mechanism of the host response and the possibility of establishing active herd immunity. ASFV is able to infect core tissues and is associated with acute death. RNA and protein samples were obtained and verified from five tissues, including the lung, spleen, liver, kidney and lymph nodes. Multiple duplicate samples were quantitatively analyzed by corresponding transcriptomic and proteomic comparison. The results showed that different tissues cooperated in responses to ASFV infection and coordinated the defence against ASFV in the form of an inflammatory cytokine storm and interferon activation. The lung and spleen were mainly involved (dominant) in the innate immune response pathway; the liver and kidney were involved in the metabolic regulatory pathway and the inflammatory response; and the lymph nodes cooperated with the liver to complete energy metabolism regulation. The key pathways and responsive genes in each tissue of the contracted pigs were comprehensively mapped by infectomics, providing further evidence to investigate the complicated tie between ASFV and host cells.

African swine fever virus genotype II in Mongolia, 2019

African swine fever (ASF) is a severe haemorrhagic disease of domestic and wild pigs caused by the African swine fever virus (ASFV). In recent years, ASF has steadily spread towards new geographical areas, reaching Europe and Asia. On January 15th, 2019, Mongolia reported its first ASF outbreak to the World Organization for Animal Health (OIE), becoming, after China, the second country in the region affected by the disease. Following an event of unusual mortality in domestic pigs in Bulgan Province, a field team visited four farms and a meat market in the region to conduct an outbreak investigation and collect samples for laboratory analysis. Different organs were examined for ASF associated lesions, and total nucleic acid was extracted for real-time PCR, virus isolation and molecular characterization. The real-time PCR results confirmed ASFV DNA in 10 out of 10 samples and ASFV was isolated. Phylogenetic analysis established that ASFVs from Mongolia belong to genotype II and serogroup 8. The viruses were identical to each other, and to domestic pig isolates identified in China and Russia, based on the comparison of five genomic targets. Our results suggest a cross-border spread of ASFV, without indicating the source of infection.

Genetic profile of African swine fever virus responsible for the 2019 outbreak in northern Malawi

Background

African swine fever (ASF) is an infectious transboundary animal disease which causes high mortality, approaching 100% in domestic pigs and it is currently considered as the most serious constraint to domestic pig industry and food security globally. Despite regular ASF outbreaks within Malawi, few studies have genetically characterized the causative ASF virus (ASFV). This study aimed at genetic characterization of ASFV responsible for the 2019 outbreak in northern Malawi. The disease confirmation was done by polymerase chain reaction (PCR) followed by molecular characterization of the causative ASFV by partial genome sequencing and phylogenetic reconstruction of the B646L (p72) gene, nucleotide alignment of the intergenic region (IGR) between I73R and I329L genes and translation of the central variable region (CVR) coded by B602L gene.

Results

All thirteen samples collected during this study in Karonga district in September 2019 were ASFV-positive and after partial genome sequencing and phylogenetic reconstruction of the B646L (p72) gene, the viruses clustered into ASFV p72 genotype II. The viruses characterized in this study lacked a GAATATATAG fragment between the I173R and the I329L genes and were classified as IGR I variants. Furthermore, the tetrameric amino acid repeats within the CVR of the B602L gene of the 2019 Malawian ASFV reported in this study had the signature BNDBNDBNAA, 100% similar to ASFV responsible for the 2013 and 2017 ASF outbreaks in Zambia and Tanzania, respectively.

Conclusions

The results of this study confirm an ASF outbreak in Karonga district in northern Malawi in September 2019. The virus was closely related to other p72 genotype II ASFV that caused outbreaks in neighboring eastern and southern African countries, emphasizing the possible regional transboundary transmission of this ASFV genotype. These findings call for a concerted regional and international effort to control the spread of ASF in order to improve nutritional and food security.