Spatio-temporal patterns and movement analysis of pigs from smallholder farms and implications for African swine fever spread, Limpopo province, South Africa

Innovative Research Offers New Hope for Managing African Swine Fever Better in Resource-Limited Smallholder Farming Settings: A Timely Update

African swine fever (ASF) in domestic pigs has, since its discovery in Africa more than a century ago, been associated with subsistence pig keeping with low levels of biosecurity. Likewise, smallholder and backyard pig farming in resource-limited settings have been notably affected during the ongoing epidemic in Eastern Europe, Asia, the Pacific, and Caribbean regions. Many challenges to managing ASF in such settings have been identified in the ongoing as well as previous epidemics. Consistent implementation of biosecurity at all nodes in the value chain remains most important for controlling and preventing ASF. Recent research from Asia, Africa, and Europe has provided science-based information that can be of value in overcoming some of the hurdles faced for implementing biosecurity in resource-limited contexts. In this narrative review we examine a selection of these studies elucidating innovative solutions such as shorter boiling times for inactivating ASF virus in swill, participatory planning of interventions for risk mitigation for ASF, better understanding of smallholder pig-keeper perceptions and constraints, modified culling, and safe alternatives for disposal of carcasses of pigs that have died of ASF. The aim of the review is to increase acceptance and implementation of science-based approaches that increase the feasibility of managing, and the possibility to prevent, ASF in resource-limited settings. This could contribute to protecting hundreds of thousands of livelihoods that depend upon pigs and enable small-scale pig production to reach its full potential for poverty alleviation and food security.

Analysis of the drivers of ASF introduction into the officially approved pig compartments in South Africa and implications for the revision of biosecurity standards

BACKGROUND

While African Swine Fever (ASF) virus has historically circulated in wild pigs and in Ornithodoros ticks in parts of South Africa, the virus has spread among domestic pigs throughout the country since 2019. South Africa's compartment system has been used as a mainstay approach to protecting the swine industry in the face of ASF. However, in 2020, two compartments broke down with ASF. The objectives of this study are to investigate the drivers for ASF introduction into the compartments, to categorize compartments by risk of ASF introduction, and to make corresponding recommendations. The relevance of risk factors for ASF introduction for each compartment were investigated among veterinarians and farm managers. The analysis of risk factors weighted according to an expert elicitation were used to categorize compartments into risk levels.

RESULTS

Drivers of disease related to human behaviors and to domestic pig management are perceived by farm managers and veterinarians of the compartments to be critical for ASF introduction into compartments in South Africa. Twenty-four units were categorized as high risk, forty-seven as medium risk, and twenty-four as low risk. "Insufficient boot and clothing biosecurity by animal health personnel" was identified as a relevant risk factor in all high risk units. Other prominent risk factors were "insufficient boot and clothing biosecurity by external people," "underreporting of suspect ASF cases," "improper hunting/ culling of wild suids inside the compartment," "un-tested introductions into the herd," and "entry and contact with free-roaming pigs." The roles of wild pigs and competent vectors are considered minimal. There is a need for revision of the compartment standards and training of compartment personnel on the standards. The major gaps identified in the standards were absence of a monitoring programme to assess biosecurity implementation and suboptimal surveillance testing and audit strategies.

CONCLUSIONS

The results of our study confirm that ASF is increasingly an anthropogenic problem. Updating the compartment standards and addressing gaps in the knowledge of compartment personnel on ASF are most critical. To enhance compliance with biosecurity measures and thus control the disease, close engagement with all stakeholders linked to the compartments is needed.

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.

Prioritisation of Provinces for African Swine Fever Intervention in South Africa through Decision Matrix Analysis

South Africa has experienced an increase in the number of African swine fever (ASF) outbreaks in domestic pigs in the last ten years. Intervention will be needed in the form of control and prevention strategies to minimise the impact of this disease in the country. The aim of this study is to prioritise which provinces resources should be allocated to for ASF intervention strategies, based on the risk factors identified as pertinent in South Africa. A multi-criteria decision analysis approach was followed using an analytic hierarchy process (AHP) method to determine the perceived risk of ASF outbreaks in domestic pigs per province. Nine risk factors applicable to the South African context were identified from literature. Data on the presence of these risk factors per province were collected from records and by means of a questionnaire. The risk factors were weighted by means of an AHP. The decision matrix determined that ASF intervention and prevention resources should be focused on Mpumalanga, Free State and Gauteng provinces in South Africa. Specific intervention strategies should be focused on the confinement of pigs, swill-feeding of pigs and buying/selling of pigs at auctions through a participatory approach with stakeholders.

Extension of Sylvatic Circulation of African Swine Fever Virus in Extralimital Warthogs in South Africa

Sylvatic circulation of African swine fever virus (ASFV) in warthogs and Ornithodoros ticks that live in warthog burrows historically occurred in northern South Africa. Outbreaks of the disease in domestic pigs originated in this region. A controlled area was declared in the north in 1935 and regulations were implemented to prevent transfer of potentially infected suids or products to the rest of the country. However, over the past six decades, warthogs have been widely translocated to the south where the extralimital animals have flourished to become an invasive species. Since 2016, there have been outbreaks of ASF in pigs outside the controlled area that cannot be linked to transfer of infected animals or products from the north. An investigation in 2008–2012 revealed that the presence of Ornithodoros ticks and ASFV in warthog burrows extended marginally across the boundary of the controlled area. We found serological evidence of ASFV circulation in extralimital warthogs further south in the central part of the country.

Spatial-Temporal Movements of Free Ranging Pigs at the Wildlife-Livestock Interface of Murchison Falls National Park, Uganda: Potential of Disease Control at a Local Scale

In many Ugandan rural communities, pigs are generally kept under traditional smallholder systems without basic biosecurity measures in place. In some instances, these systems are at the livestock-wildlife interface, as it is the case in Nwoya district, which is bordered by Murchison Falls National Park (MFNP). This pig system has potential for the maintenance and transmission of pathogens like African swine fever (ASF) between different herds, and also with wild pigs (warthogs and bushpigs). In this paper, we describe the spatial and temporal pattern of the movements of free ranging domestic pigs in a rural setting in Northern Uganda where ASF is endemic. We also determine their use of habitat to highlight the potential interaction hotspots between domestic pigs and between domestic and wild pig populations. We fitted 10 free-ranging domestic pigs owned by different homesteads with GPS harnesses during rainy and dry seasons. The pig home range, daily distance, activity pattern and habitat use were calculated. Our results show that the maximum area covered (MCP 100%) by the pigs varied between 35,965 and 475,077 m2. The core area varied from 1,317 to 50,769 m2. The pigs' home ranges were significantly bigger during the dry season than during the rainy season (Wilcoxon test, W = 22, p = 0.04). The mean full day (24 h) distance was longer in the dry season than in the rainy season (Student test, t = 2.7, p = 0.03). The pigs were mostly located within their own homestead, but they also used other homesteads, grass and crop fields. This study highlights that free-ranging domestic pigs may cover a wide area, especially during the dry season. Interestingly, the home range of pigs from different herds may overlap with areas used by wild pigs which share crops and other resources in this area. This study provides insights into a better understanding of the potential for spread of diseases such as ASF at small-scale and can be used to raise awareness of such risks and to better target implementation of preventive measures.

An outbreak of African swine fever in small-scale pigs, Gauteng, South Africa, July 2020

OBJECTIVES

Since 2012, outbreaks of African swine fever (ASF) in domestic pigs have increased outside of South Africa's ASF control zone. This study describes the epidemiological investigation and findings of an ASF outbreak in a small-scale pig unit in Gauteng Province and makes recommendations to prevent future outbreaks.

METHODS

PCR testing and molecular analysis were performed on pig tissue samples. Veterinary services conducted epidemiological investigations, forward and backward tracing, and surveillance. Farm management and biosecurity practices were assessed. Quarantine, culling, carcass disposal, and disinfection were implemented.

RESULTS

ASF virus genotype I was detected. A concurrent ASF outbreak in neighbouring Mpumalanga Province was identified as a possible source. Inadequate biosecurity measures probably facilitated viral transmission. Potential mechanisms for the introduction of the ASF virus include swill feeding practices, free roaming of pigs, scavenging, illegal slaughter, and trade of pig products within the community.

CONCLUSIONS

Molecular typing of the ASF virus linked the outbreak to an ongoing ASF outbreak in Mpumalanga Province. Pig enterprises with poor biosecurity practices may face greater risk of ASF introduction. Small-scale pig keepers should be targeted for ASF awareness and education campaigns. Innovative and cost-effective biosecurity solutions are needed in this resource-poor setting.

Investigation into eradication of African swine fever in domestic pigs from a previous outbreak (2016/17) area of South Africa

A serological survey was conducted to evaluate the eradication of African swine fever (ASF) infection eighteen months after clinical surveillance and selective culling had been completed during domestic cycle outbreaks in parts of South Africa in 2016/17. Three hundred and twenty-two serum samples from 85 pig keepers were collected in the study area and tested for the presence of antibodies against the ASF virus (ASFV). None of the samples contained detectable levels of antibodies against ASFV. These results together with the findings from clinical surveillance following culling activities suggest that the disease had been eradicated from the domestic pig population in this area following the outbreaks. Questionnaire responses from the pig keepers in this area highlighted the need to implement basic biosecurity measures in smallholder pig keepers to prevent outbreaks of ASF in South Africa.

Investigation of African swine fever outbreaks in pigs outside the controlled areas of South Africa, 2012-2017

South Africa historically experienced sporadic African swine fever (ASF) outbreaks in domestic pigs in the northern parts of the country. This was subsequently indicated to be because of spillover from the sylvatic cycle of ASF between warthog and tampans (soft ticks) in the area. South Africa declared this area an ASF-controlled area in 1935, and the area is still controlled in terms of the Animal Diseases Act, 1984 (Act 35 of 1984). Two main epidemics of ASF in domestic pigs were identified outside of the South African ASF-controlled area. The first occurred in 2012 with outbreaks in Gauteng and Mpumalanga provinces, and the second occurred in 2016-2017 with outbreaks in the North West, Free State and Northern Cape provinces. These were the first ASF epidemics in South Africa associated with transmission of the disease via a domestic cycle. This study found that the spread of ASF in these epidemics was mainly via auctions, swill feeding and scavenging. These three aspects need to be addressed in terms of awareness and education on the disease including implementation of biosecurity measures in order to prevent future ASF outbreaks in South Africa. Specific biosecurity measures should be implemented in the semi-commercial sector to prevent ASF-infected pigs and pig products from being moved to naïve pigs and therefore spreading the disease.

Systematic Review of Important Viral Diseases in Africa in Light of the 'One Health' Concept

Emerging and re-emerging viral diseases are of great public health concern. The recent emergence of Severe Acute Respiratory Syndrome (SARS) related coronavirus (SARS-CoV-2) in December 2019 in China, which causes COVID-19 disease in humans, and its current spread to several countries, leading to the first pandemic in history to be caused by a coronavirus, highlights the significance of zoonotic viral diseases. Rift Valley fever, rabies, West Nile, chikungunya, dengue, yellow fever, Crimean-Congo hemorrhagic fever, Ebola, and influenza viruses among many other viruses have been reported from different African countries. The paucity of information, lack of knowledge, limited resources, and climate change, coupled with cultural traditions make the African continent a hotspot for vector-borne and zoonotic viral diseases, which may spread globally. Currently, there is no information available on the status of virus diseases in Africa. This systematic review highlights the available information about viral diseases, including zoonotic and vector-borne diseases, reported in Africa. The findings will help us understand the trend of emerging and re-emerging virus diseases within the African continent. The findings recommend active surveillance of viral diseases and strict implementation of One Health measures in Africa to improve human public health and reduce the possibility of potential pandemics due to zoonotic viruses.

Simulation modeling of influenza transmission through backyard pig trade networks in a wildlife/livestock interface area

Influenza constitutes a challenge to animal and human health. It is a highly contagious disease with wildlife reservoirs and considered as endemic among swine populations. Pigs are crucial in the disease dynamics due to their capacity to generate new reassortant viruses. The risk of informal animal trade in the spread of zoonotic diseases is well recognized worldwide. Nevertheless, the contribution of the backyard pig trade network in the transmission of influenza in a wildlife/livestock interface area is unknown. This study provides the first simulation of influenza transmission based on backyard farm connections in Mexico. A susceptible-infectious-recovered (SIR) model was implemented using the Epimodel software package in R, and 260 backyard farms were considered as nodes. Three different scenarios of connectivity (low, medium, and high) mediated by trade were generated and compared. Our results suggest that half of the pig population were infected within 5 days in the high connectivity scenario and the number of infected farms was approximately 65-fold higher compared to the low connected one. The consequence of connectivity variations directly influenced both time and duration of influenza virus transmission. Therefore, high connectivity driven by informal trade constitutes a significant risk to animal health. Trade patterns of animal movements are complex. This approach emphasizes the importance of pig movements and spatial dynamics among backyard production, live animal markets, and wildlife.

African swine fever: Update on Eastern, Central and Southern Africa

Control of African swine fever (ASF) in countries in Eastern, Central and Southern Africa (ECSA) is particularly complex owing to the presence of all three known epidemiological cycles of maintenance of the virus, namely an ancient sylvatic cycle involving the natural hosts and vectors of the disease as well as domestic cycles with and without involvement of natural vectors. While the situation is well documented in some of the countries, for others very little information is available. In spite of the unfavourable ASF situation, the pig population in the sub-region has grown exponentially in recent decades and is likely to continue to grow in response to rapid urban growth resulting in increasing demand for animal protein by populations that are no longer engaged in livestock production. Better management of ASF will be essential to permit the pig sector to reach its full potential as a supplier of high quality protein and a source of income to improve livelihoods and create wealth. No vaccine is currently available and it is likely that, in the near future, the sub-region will continue to rely on the implementation of preventive measures, based on the epidemiology of the disease, to avoid both the devastating losses that outbreaks can cause and the risk the sub-region poses to other parts of Africa and the world. The current situation in the ECSA sub-region is reviewed and gaps in knowledge are identified in order to support ongoing strategy development for managing ASF in endemic areas.