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African wild suids consist of several endemic species that represent ancient members of the family Suidae and have colonized diverse habitats on the African continent. However, limited genomic resources for African wild suids hinder our understanding of their evolution and genetic diversity. In this study, we assembled high-quality genomes of a common warthog (Phacochoerus africanus), a red river hog (Potamochoerus porcus), as well as an East Asian Diannan small-ear pig (Sus scrofa). Phylogenetic analysis showed that common warthog and red river hog diverged from their common ancestor around the Miocene/Pliocene boundary, putatively predating their entry into Africa. We detected species-specific selective signals associated with sensory perception and interferon signaling pathways in common warthog and red river hog, respectively, which contributed to their local adaptation to savannah and tropical rainforest environments, respectively. The structural variation and evolving signals in genes involved in T-cell immunity, viral infection, and lymphoid development were identified in their ancestral lineage. Our results provide new insights into the evolutionary histories and divergent genetic adaptations of African suids.

African swine fever (ASF) caused by the African swine fever virus (ASFV) is ranked by OIE as the most important source of mortality in domestic pigs globally and is indigenous to African wild suids and soft ticks. Despite two ASFV genotypes causing economically devastating epidemics outside the continent since 1961, there have been no genome-level analyses of virus evolution in Africa. The virus was recently transported from south-eastern Africa to Georgia in 2007 and has subsequently spread to Russia, eastern Europe, China, and south-east Asia with devastating socioeconomic consequences. To date, two of the 24 currently described ASFV genotypes defined by sequencing of the p72 gene, namely genotype I and II, have been reported outside Africa, with genotype II being responsible for the ongoing pig pandemic. Multiple complete genotype II genome sequences have been reported from European, Russian and Chinese virus isolates but no complete genome sequences have yet been reported from Africa. We report herein the complete genome of a Tanzanian genotype II isolate, Tanzania/Rukwa/2017/1, collected in 2017 and determined using an Illumina short read strategy. The Tanzania/Rukwa/2017/1 sequence is 183,186 bp in length (in a single contig) and contains 188 open reading frames. Considering only un-gapped sites in the pairwise alignments, the new sequence has 99.961% identity with the updated Georgia 2007/1 reference isolate (FR682468.2), 99.960% identity with Polish isolate Pol16_29413_o23 (MG939586) and 99.957% identity with Chinese isolate ASFV-wbBS01 (MK645909.1). This represents 73 single nucleotide polymorphisms (SNPs) relative to the Polish isolate and 78 SNPs with the Chinese genome. Phylogenetic analysis indicated that Tanzania/Rukwa/2017/1 clusters most closely with Georgia 2007/1. The majority of the differences between Tanzania/Rukwa/2017/1 and Georgia 2007/1 genotype II genomes are insertions/deletions (indels) as is typical for ASFV. The indels included differences in the length and copy number of the terminal multicopy gene families, MGF 360 and 110. The Rukwa2017/1 sequence is the first complete genotype II genome from a precisely mapped locality in Africa, since the exact origin of Georgia2007/1 is unknown. It therefore provides baseline information for future analyses of the diversity and phylogeography of this globally important genetic sub-group of ASF viruses.

African swine fever (ASF) is a severe haemorrhagic disease of domestic pigs caused by ASF virus (ASFV). ASFV is transmitted by soft ticks (Ornithodoros moubata complex group) and by direct transmission. In Africa, ASF is maintained in transmission cycles of asymptomatic infection involving wild suids, mainly warthogs (Phacochoerus africanus). ASF outbreaks have been reported in many parts of Tanzania; however, active surveillance has been limited to pig farms in a few geographical locations. There is an information gap on whether and where the sylvatic cycle may occur independently of domestic pigs. To explore the existence of a sylvatic cycle in Saadani National Park in Tanzania, blood and serum samples were collected from 19 warthogs selected using convenience sampling along vehicle‐accessible transects within the national park. The ticks were sampled from warthog burrows. Blood samples and ticks were subjected to ASFV molecular diagnosis (PCR) and genotyping, and warthog sera were subjected to serological (indirect ELISA) testing for ASFV antibody detection. All warthog blood samples were PCR‐negative, but 16/19 (84%) of the warthog sera were seropositive by ELISA confirming exposure of warthogs to ASFV. Of the ticks sampled, 20/111 (18%) were positive for ASFV by conventional PCR. Sequencing of the p72 virus gene fragments showed that ASF viruses detected in ticks belonged to genotype XV. The results confirm the existence of a sylvatic cycle of ASFV in Saadani National Park, Tanzania, that involves ticks and warthogs independent of domestic pigs. Our findings suggest that genotype XV previously reported in 2008 in Tanzania is likely to be widely distributed and involved in both wild and domestic infection cycles. Whole‐genome sequencing and analysis of the ASFV genotype XV circulating in Tanzania is recommended to determine the phylogeny of the viruses.

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As warthog (Phacochoerus africanus) has innate immunity against African swine fever (ASF), it is critical to understand the evolutionary novelty of warthog to explain its specific ASF resistance. Here, we present two completed new genomes of one warthog and one Kenyan domestic pig, as the fundamental genomic references to decode the genetic mechanism on ASF tolerance. Our results indicated, multiple genomic variations, including gene losses, independent contraction and expansion of specific gene families, likely moulded warthog’s genome to adapt the environment. Importantly, the analysis of the presence and absence of genomic sequences revealed that, the warthog genome had a DNA sequence absence of the lactate dehydrogenase B (LDHB) gene on chromosome 2 compared to the reference genome. The overexpression and siRNA of LDHB indicated that its inhibition on the replication of ASFV. Combining with large-scale sequencing data of 123 pigs from all over the world, contraction and expansion of TRIM genes families revealed that TRIM family genes in the warthog genome were potentially responsible for its tolerance to ASF. Our results will help further improve the understanding of genetic resistance ASF in pigs.

In this study, we describe an African swine fever genotype IX virus (ASFV-Kenya-1033-IX), which was isolated from a domestic pig in Western Kenya during a reported outbreak, including efficiency of virus replication, in vivo virulence, and genome stability in pulmonary alveolar macrophages (PAM) and in a wild boar cell line (WSL). The ASFV-Kenya-1033-IX stock, which underwent multiple passages in WSL (more than 20), retained its ability to replicate in primary macrophages and it also retained the virulence in vivo. At the genomic level, only a few single nucleotide differences were observed between the macrophage and WSL-grown virus. Thus, we propose that the WSL cell line is suitable to produce live attenuated ASFV vaccine candidates based on this isolate and probably of similar viruses. The genome sequences for ASFV-Kenya-1033-IX grown in macrophages and in WSL cells was submitted to GenBank and a challenge model based on this isolate was set up, which will aid the development of vaccines against genotype IX ASFV circulating in Eastern and Central 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.

Swine leukocyte antigen (SLA) plays a central role in controlling the immune response by discriminating self and foreign antigens and initiating an immune response. Studies on SLA polymorphism have demonstrated associations between SLA allelic variants, immune response, and disease resistance. The SLA polymorphism is due to host-pathogen co-evolution resulting in improved adaptation to diverse environments making SLA a crucial genomic region for comparative diversity studies. Although locally-adapted African pigs have small body sizes, they possess increased resilience under harsh environmental conditions and robust immune systems with reported tolerance to some diseases, including African swine fever. However, data on the SLA diversity in these pigs are not available. We characterized the SLA of unrelated locally-adapted domestic pigs from Homa Bay, Kenya, alongside exotic pigs and warthogs. We undertook SLA comparative diversity of the functionally expressed SLA class I (SLA-1, SLA-2) and II (DQB1) repertoires in these three suids using the reverse transcription polymerase chain reaction (RT-PCR) sequence-based typing (SBT) method. Our data revealed higher genetic diversity in the locally-adapted pigs and warthogs compared to the exotic pigs. The nucleotide substitution rates were higher in the peptide-binding regions of the SLA-1, SLA-2, and DQB1 loci, indicative of adaptive evolution. We obtained high allele frequencies in the three SLA loci, including some breed-specific private alleles, which could guide breeders to increase their frequency through selection if confirmed to be associated with enhanced resilience. Our study contributes to the growing body of knowledge on genetic diversity in free-ranging animal populations in their natural environment, availing the first DQB1 gene data from locally-adapted Kenyan pigs.

Swine leukocyte antigen (SLA) plays a central role in controlling the immune response by discriminating self and foreign antigens and initiating an immune response. Studies on SLA polymorphism have demonstrated associations between SLA allelic variants, immune response, and disease resistance. The SLA polymorphism is due to host-pathogen co-evolution resulting in improved adaptation to diverse environments making SLA a crucial genomic region for comparative diversity studies. Although locally-adapted African pigs have small body sizes, they possess increased resilience under harsh environmental conditions and robust immune systems with reported tolerance to some diseases, including African swine fever. However, data on the SLA diversity in these pigs are not available. We characterized the SLA of unrelated locally-adapted domestic pigs from Homa Bay, Kenya, alongside exotic pigs and warthogs. We undertook SLA comparative diversity of the functionally expressed SLA class I (SLA-1, SLA-2) and II (DQB1) repertoires in these three suids using the reverse transcription polymerase chain reaction (RT-PCR) sequence-based typing (SBT) method. Our data revealed higher genetic diversity in the locally-adapted pigs and warthogs compared to the exotic pigs. The nucleotide substitution rates were higher in the peptide-binding regions of the SLA-1, SLA-2, and DQB1 loci, indicative of adaptive evolution. We obtained high allele frequencies in the three SLA loci, including some breed-specific private alleles, which could guide breeders to increase their frequency through selection if confirmed to be associated with enhanced resilience. Our study contributes to the growing body of knowledge on genetic diversity in free-ranging animal populations in their natural environment, availing the first DQB1 gene data from locally-adapted Kenyan pigs.

African Swine Fever (ASF) was reported in domestic pigs in China in 2018. This highly contagious viral infection with no effective vaccine reached pandemic proportions by 2019, substantially impacting protein availability in the same region where the COVID-19 pandemic subsequently emerged. We discuss the genesis, spread, and wide-reaching impacts of an epidemic in a vital livestock species, noting parallels and potential contributions to ignition of COVID-19. We speculate about follow-on impacts of these pandemics on global public health infrastructure and suggest intervention strategies using a cost: benefit approach for low-risk, massive-impact events. We note that substantive changes in how the world reacts to potential threats will be required to overcome catastrophes driven by climate change, food insecurity, lack of surveillance infrastructure and other gaps. We note that a One Health approach creating collaborative processes connecting expertise in human, animal, and environmental health is essential for combating future global health crises.

Astroviruses (AstVs) are widely distributed and are associated with gastroenteritis in human and animals. The knowledge of the genetic diversity and epidemiology of AstVs in Africa is limited. This study aimed to characterize astroviruses in asymptomatic smallholder piglets in Kenya and Uganda. Twenty-four samples were randomly selected from a total of 446 piglets aged below 6 months that were initially collected for rotavirus study and sequenced for whole genome analysis. Thirteen (13/24) samples had contigs with high identity to genus Mamastrovirus. Analysis of seven strains with complete (or near complete) AstV genome revealed variable nucleotide and amino acid sequence identities with known porcine astrovirus (PoAstV) strains. The U083 and K321 strains had nucleotide sequence identities ranging from 66.4 to 75.4% with the known PoAstV2 strains, U460 strain had nucleotide sequence identities of 57.0 to 65.1% regarding the known PoAstV3, and K062, K366, K451, and K456 strains had nucleotide sequence identities of 63.5 to 80% with the known PoAstV4 strains. The low sequence identities (&lt, 90%) indicate that novel genotypes of PoAstVs are circulating in the study area. Recombination analysis using whole genomes revealed evidence of multiple recombination events in PoAstV4, suggesting that recombination might have contributed to the observed genetic diversity. Linear antigen epitope prediction and a comparative analysis of capsid protein of our field strains identified potential candidate epitopes that could help in the design of immuno-diagnostic tools and a subunit vaccine. These findings provide new insights into the molecular epidemiology of porcine astroviruses in East Africa.

Astroviruses (AstVs) are occurs globally and are common causes of gastroenteritis in human and animals. The genetic diversity and epidemiology of AstVs in Africa is not well known, hence, we aimed to genetically characterize astroviruses in asymptomatic smallholder piglets in East Africa. Twenty-four samples randomly selected from 446 piglets (

Background African swine fever (ASF), a highly contagious hemorrhagic disease, affects domestic pigs in the Democratic Republic of Congo (DRC) where regular outbreaks are reported leading to high mortality rates approaching 100% in the affected regions. No study on the characteristics of the complete genome of strains responsible for ASF outbreaks in the South Kivu province of DRC is available, limited a better understanding of molecular evolution and spread of this virus within the country. The present study aimed at determining the complete genome sequence of ASFV strains genotype X involved in 2018–2019 ASF disease outbreaks in South Kivu province of DRC. Materials and methods Genomic DNA of a spleen sample from an ASFV genotype X-positive domestic pig in Uvira, during the 2018–2019 outbreaks in South Kivu, was sequenced using the Illumina HiSeq X platform. Obtained trimmed reads using Geneious Prime 2020.0.4 were blasted against a pig reference genome then contigs were generated from the unmapped reads enriched in ASFV DNA using Spades implemented in Geneious 2020.0.4. The assembly of the complete genome sequence of ASFV was achieved from the longest overlapping contigs. The new genome was annotated with the genome annotation transfer utility (GATU) software and the CLC Genomics Workbench 8 software was further used to search for any ORFs that failed to be identified by GATU. Subsequent analyses of the newly determined Uvira ASFV genotype X genome were done using BLAST for databases search, CLUSTAL W for multiple sequences alignments and MEGA X for phylogeny. Results 42 Gbp paired-end reads of 150 bp long were obtained containing about 0.1% of ASFV DNA. The assembled Uvira ASFV genome, termed Uvira B53, was 180,916 bp long that could be assembled in 2 contigs. The Uvira B53genome had a GC content of 38.5%, encoded 168 open reading frames (ORFs) and had 98.8% nucleotide identity with the reference ASFV genotype X Kenya 1950. The phylogenetic relationship with selected representative genomes clustered the Uvira B53 strain together with ASFV genotype X reported to date (Kenya 1950 and Ken05/Tk1). Multiple genome sequences comparison with the two reference ASFV genotype X strains showed that 130 of the 168 ORFs were fully conserved in the Uvira B53. The other 38 ORFs were divergent mainly due to SNPs and indels (deletions and insertions). Most of 46 multigene family (MGF) genes identified were affected by various genetic variations. However, 8 MGF ORFs present in Kenya 1950 and Ken05/Tk1 were absent from the Uvira B53 genome including three members of MGF 360, four of MGF 110 and one of MGF 100 while one MGF ORF (MGF 360-1L) at the left end of the genome was truncated in Uvira B53. Moreover, ORFs DP96R and p285L were also absent in the Uvira B53 genome. In contrast, the ORF MGF 110-5L present in Uvira B53 and Ken05/Tk1 was missing in Kenya 1950. The analysis of the intergenic region between the I73R and I329L genes also revealed sequence variations between the three genotype X strains mainly characterized by a deletion of 69 bp in Uvira B53 and 36 bp in Kenya 1950, compared to Ken05/Tk1. Assessment of the CD2v (EP402R) antigen unveiled the presence of SNPs and indels particularly in the PPPKPY tandem repeat region between selected variants representing the eight serogroups reported to date. Uvira B53 had identical CD2v variable region to the Uganda (KM609361) strain, the only other ASFV serogroup 7 reported to date. Conclusion We report the first complete genome sequence of an African swine fever virus (ASFV) p72 genotype X and CD2v serogroup 7, termed Uvira B53. This study provides additional insights on genetic characteristics and evolution of ASFV useful for tracing the geographical spread of ASF and essential for improved design of control and management strategies against ASF.

The persistence of African swine fever virus (ASFV) in endemic areas, with small-scale but regular outbreaks in domestic pigs, is not well understood. ASFV has not been detected using conventional diagnosis in these pigs or adjacent populations of resistant African wild pigs, that could act as potential carriers during the outbreaks. However, such data are crucial for the design of evidence-based control strategies. We conducted cross-sectional (1107 pigs) and longitudinal (100 pigs) monitoring of ASFV prevalence in local pigs in Kenya and Uganda. The horizontal survey revealed no evidence of ASFV in the serum or blood using either conventional or real-time PCR. One pig consistently tested positive using ELISA, but negative using PCR assays on blood. Interestingly, the isotype of the antibodies from this animal were strongly IgA biased relative to control domestic pigs and warthogs, suggesting a role for mucosal immunity. The tissues from this pig were positive by PCR following post-mortem. Internal organ tissues of 44 healthy pigs (28 sentinel pigs and 16 pigs from slaughter slabs) were tested with four different PCR assays; 15.9 % were positive for ASFV suggesting that healthy pigs carrying ASFV exist in the swine population in the study area. P72 and p54 genotyping of ASFV revealed very limited diversity: all were classified in genotype IX at both loci, as were virtually all viruses causing recent ASF outbreaks in the region. Our study suggests that carrier pigs may play a role in ASF disease outbreaks, although the triggers for outbreaks remain unclear and require further investigation. This study significantly increases scientific knowledge of the epidemiology of ASF in the field in Africa, which will contribute to the design of effective surveillance and control strategies.

We applied social network analysis to pig trader networks on the Kenya-Uganda border. Social network analysis is a recently developed tool, which is useful for understanding value chains and improving disease control policies. We interviewed a sample of 33 traders about their experiences with trade and African swine fever (ASF), analyzed the networks they generated in purchasing pigs and selling pork and their potential contribution to modulating dissemination of the ASF virus (ASFV). The majority of the traders were aware of clinical signs of ASF and the risk of trade transmitting ASFV. Most said they avoided buying pigs from ASF outbreak villages or sick pigs but their experiences also indicated that inadvertent purchase was relatively common. Traders had early knowledge of outbreaks since they were contacted by farmers who had heard rumours and wanted to sell their pigs to avoid the risk of them dying. Individual traders bought pigs in up to nine villages, and up to six traders operated in a village. Although each trade typically spanned less than 5km, networks of the various traders, comprising movements of pigs from source villages to slaughter slabs/sites and retail outlets, and movement of pork to villages where it was consumed, linked up indirectly across the 100km×50km study area and revealed several trade pathways across the Kenya-Uganda border. ASF could potentially spread across this area and beyond through sequential pig and pork transactions. Regulation of the pig and pork trade was minimal in practice. The risk of ASFV being spread by traders was compounded by their use of poorly constructed slaughter slabs/sites with open drainage, ineffective or non-existent meat inspection services, lack of provision for biosecurity in the value chain, and sales of pork to customers who were unaware of the risks to their own pigs from contact with ASF infected pork. More effective regulation is warranted. However, limitations on government capacity, together with the strong self-interest that established traders have in reducing the disruption and financial losses that outbreaks cause, highlight the importance of governments and traders co-developing an approach to ASF control. Formation of trader organizations or common interest groups warrants government support as an important step in engaging traders in developing and implementing effective approaches to reduce the risk of ASF outbreaks.

Globally, malaria remains one of the most important vector-borne diseases despite the extensive use of vector control, including indoor residual spraying (IRS) and insecticide-treated nets (ITNs). These control methods target endophagic vectors, whereas some malaria vectors, such as Anopheles arabiensis, preferentially feed outdoors on cattle, making it a complicated vector to control using conventional strategies. Our study evaluated whether treating cattle with a capsule containing the active ingredient (AI) fipronil could reduce vector density and sporozoite rates, and alter blood feeding behavior, when applied in a small-scale field study. A pilot field study was carried out in the Samia District, Western Kenya, from May to July 2015. Four plots, each comprised of 50 huts used for sleeping, were randomly designated to serve as control or treatment. A week before cattle treatment, baseline mosquito collections were performed inside the houses using mechanical aspirators. Animals in the treatment (and buffer) were administered a single oral application of fipronil at ∼0.5 mg/kg of body weight. Indoor mosquito collections were performed once a week for four weeks following treatment. Female mosquitoes were first identified morphologically to species complex, followed by PCR-based methods to obtain species identity, sporozoite presence, and the host source of the blood meal. All three species of anophelines found in the study area (An. gambiae s.s., An. arabiensis, An. funestus s.s.) were actively transmitting Plasmodium falciparum during the study period. The indoor resting density of An. arabiensis was significantly reduced in treatment plot one at three weeks post-treatment (T1) (efficacy = 89%; T1 density = 0.08, 95% credibility intervals [0.05, 0.10]; control plot density = 0.78 [0.22, 0.29]) and at four weeks post-treatment (efficacy = 64%; T1 density = 0.16 [0.08, 0.14]; control plot density = 0.48 [0.17, 0.22]). The reduction of An. arabiensis mosquitoes captured in the treatment plot two was higher: zero females were collected after treatment. The indoor resting density of An. gambiae s.s. was not significantly different between the treatment (T1, T2) and their corresponding control plots (C1, C2). An. funestus s.s. showed an increase in density over time. The results of this preliminary study suggest that treating cattle orally with fipronil, to target exophagic and zoophagic malaria vectors, could be a valuable control strategy to supplement existing vector control interventions which target endophilic anthropophilic species.

Background Wildebeest associated malignant catarrhal fever (WA-MCF) is a fatal disease of cattle. Outbreaks are seasonal and associated with close interaction between cattle and calving wildebeest. In Kenya, WA-MCF has a dramatic effect on cattle-keepers who lose up to 10% of their cattle herds per year. The objective of this study was to report the impact of WA-MCF on a commercial ranch and assess the performance of clinical diagnosis compared to laboratory diagnosis as a disease management tool. A retrospective study of WA-MCF in cattle was conducted from 2014 to 2016 at Kapiti Plains Ranch Ltd., Kenya. During this period, 325 animals showed clinical signs of WA-MCF and of these, 123 were opportunistically sampled. In addition, 51 clinically healthy animals were sampled. Nested polymerase chain reaction (PCR) and indirect enzyme linked immunosorbent assay (ELISA) were used to confirm clinically diagnosed cases of WA-MCF. A latent class model (LCM) was used to evaluate the diagnostic parameters of clinical diagnosis and the tests in the absence of a gold standard. Results By PCR, 94% (95% C.I. 89–97%) of clinically affected animals were positive to WA-MCF while 63% (95% C.I. 54–71%) were positive by indirect ELISA. The LCM demonstrated the indirect ELISA had poor sensitivity 63.3% (95% PCI 54.4–71.7%) and specificity 62.6% (95% PCI 39.2–84.9%) while the nested PCR performed better with sensitivity 96.1% (95% PCI 90.7–99.7%) and specificity 92.9% (95% PCI 76.1–99.8%). The sensitivity and specificity of clinical diagnosis were 99.1% (95% PCI 96.8–100.0%) and 71.5% (95% PCI 48.0–97.2%) respectively. Conclusions Clinical diagnosis was demonstrated to be an effective method to identify affected animals although animals may be incorrectly classified resulting in financial loss. The study revealed indirect ELISA as a poor test and nested PCR to be a more appropriate confirmatory test for diagnosing acute WA-MCF. However, the logistics of PCR make it unsuitable for field diagnosis of WA-MCF. The future of WA-MCF diagnosis should be aimed at development of penside techniques, which will allow for fast detection in the field. Electronic supplementary material The online version of this article (10.1186/s12917-019-1818-8) contains supplementary material, which is available to authorized users.

Pig movements play a significant role in the spread of economically important infectious diseases such as the African swine fever. Characterization of movement networks between pig farms and through other types of farm and household enterprises that are involved in pig value chains can provide useful information on the role that different participants in the networks play in pathogen transmission. Analysis of social networks that underpin these pig movements can reveal pathways that are important in the transmission of disease, trade in commodities, the dissemination of information and the influence of behavioural norms. We assessed pig movements among pig keeping households within West Kenya and East Uganda and across the shared Kenya-Uganda border in the study region, to gain insight into within-country and trans-boundary pig movements. Villages were sampled using a randomized cluster design. Data were collected through interviews in 2012 and 2013 from 683 smallholder pig-keeping households in 34 villages. NodeXL software was used to describe pig movement networks at village level. The pig movement and trade networks were localized and based on close social networks involving family ties, friendships and relationships with neighbours. Pig movement network modularity ranged from 0.2 to 0.5 and exhibited good community structure within the network implying an easy flow of knowledge and adoption of new attitudes and beliefs, but also promoting an enhanced rate of disease transmission. The average path length of 5 defined using NodeXL, indicated that disease could easily reach every node in a cluster. Cross-border boar service between Uganda and Kenya was also recorded. Unmonitored trade in both directions was prevalent. While most pig transactions in the absence of disease, were at a small scale (5km) and characterized by regular agistment, most pig sales during ASF outbreaks were to traders or other farmers from outside the sellers' village at a range of10km. The close social relationships between actors in pig movement networks indicate the potential for possible interventions to develop shared norms and mutually accepted protocols amongst smallholder pig keepers to better manage the risk of ASF introduction and transmission.

A study was undertaken along the Kenya-Uganda border in four districts of Tororo and Busia (Uganda) and Busia and Teso (Kenya) to understand smallholder farmers' knowledge, practices and awareness of biosecurity measures. Information was collected by administering questionnaires to 645 randomly selected pig households in the study area. In addition, focus group discussions were carried out in 12 villages involving 248 people using a standardized list of questions. The outcome suggested that there was a very low level of awareness of biosecurity practices amongst smallholder farmers. We conclude that adoption of specific biosecurity practices by smallholder farmers is feasible but requires institutional support. There is a clear requirement for government authorities to sensitize farmers using approaches that allow active participation of farmers in the design, planning and implementation of biosecurity practices to enable enhanced adoption.

The genetic diversity of African pigs, whether domestic or wild has not been widely studied and there is very limited published information available. Available data suggests that African domestic pigs originate from different domestication centers as opposed to international commercial breeds. We evaluated two domestic pig populations in Western Kenya, in order to characterize the genetic diversity, breed composition and admixture of the pigs in an area known to be endemic for African swine fever (ASF). One of the reasons for characterizing these specific populations is the fact that a proportion of indigenous pigs have tested ASF virus (ASFv) positive but do not present with clinical symptoms of disease indicating some form of tolerance to infection. Pigs were genotyped using either the porcine SNP60 or SNP80 chip. Village pigs were sourced from Busia and Homabay counties in Kenya. Because bush pigs (Potamochoerus larvatus) and warthogs (Phacochoerus spp.) are known to be tolerant to ASFv infection (exhibiting no clinical symptoms despite infection), they were included in the study to assess whether domestic pigs have similar genomic signatures. Additionally, samples representing European wild boar and international commercial breeds were included as references, given their potential contribution to the genetic make-up of the target domestic populations. The data indicate that village pigs in Busia are a non-homogenous admixed population with significant introgression of genes from international commercial breeds. Pigs from Homabay by contrast, represent a homogenous population with a "local indigenous' composition that is distinct from the international breeds, and clusters more closely with the European wild boar than African wild pigs. Interestingly, village pigs from Busia that tested negative by PCR for ASFv genotype IX, had significantly higher local ancestry (>54%) compared to those testing positive, which contained more commercial breed gene introgression. This may have implication for breed selection and utilization in ASF endemic areas. A genome wide scan detected several regions under preferential selection with signatures for pigs from Busia and Homabay being very distinct. Additionally, there was no similarity in specific genes under selection between the wild pigs and domestic pigs despite having some broad areas under similar selection signatures. These results provide a basis to explore possible genetic determinants underlying tolerance to infection by ASFv genotypes and suggests multiple pathways for genetically mediated ASFv tolerance given the diversity of selection signatures observed among the populations studied.

Twelve complete African swine fever virus (ASFV) genome sequences are currently publicly available and these include only one sequence from East Africa. We describe genome sequencing and annotation of a recent pig-derived p72 genotype IX, and a tick-derived genotype X isolate from Kenya using the Illumina platform and comparison with the Kenya 1950 isolate. The three genomes constitute a cluster that was phylogenetically distinct from other ASFV genomes, but 98–99 % conserved within the group. Vector-based compositional analysis of the complete genomes produced a similar topology. Of the 125 previously identified ‘core’ ASFV genes, two ORFs of unassigned function were absent from the genotype IX sequence which was 184 kb in size as compared to 191 kb for the genotype X. There were multiple differences among East African genomes in the 360 and 110 multicopy gene families. The gene corresponding to 360-19R has transposed to the 5′ variable region in both genotype X isolates. Additionally, there is a 110 ORF in the tick-derived genotype X isolate formed by fusion of 13L and 14L that is unique among ASFV genomes. In future, functional analysis based on the variations in the multicopy families may reveal whether they contribute to the observed differences in virulence between genotpye IX and X viruses. © 2015, Springer Science+Business Media New York.

A cross-sectional survey was carried out to assess risk factors associated with occurrence of African swine fever (ASF) outbreaks in smallholder pig farms in four districts along Kenya-Uganda border. Information was collected by administering questionnaires to 642 randomly selected pig households in the study area. The study showed that the major risk factors that influenced ASF occurrence were purchase of pigs in the previous year (p

The central variable region (CVR) within the B602L gene of the African swine fever virus (ASFV) is highly polymorphic within the 23 ASFV genotypes defined by sequencing of the C-terminal end of the p72 locus. Sequencing the p54 gene further discriminates ASFV genotypes that are conserved at the p72 locus. Variation in the thymidine kinase locus is a novel additional tool for ASFV genotyping whose application for this purpose is described for the first time herein. We evaluated genetic variation at these four polymorphic loci in 39 ASFV isolates obtained from outbreaks in Kenya and a region of Eastern Uganda between 2011 and 2013. Analysis of the p72 and p54 loci revealed high genetic conservation among these isolates; all clustered within p72 genotype IX and were similar to isolates associated with earlier outbreaks in East Africa. The thymidine kinase gene of the Kenyan isolates in this study were distinct relative to Southern African isolates and synonymous substitutions were observed among viruses from central Kenya. Analysis of the CVR within the B602L gene revealed two previously unknown polymorphisms that were restricted to Western Kenya and Eastern Uganda. A novel variant was revealed within CVR subgroup XXIV and a novel CVR subgroup XXIVa that contains tetrameric repeat F which has previously only been associated with p72 genotype I, was also identified for the first time in East Africa. Phylogeographic analysis of isolates based on CVR polymorphisms revealed rapid evolution and dissemination of variants present within ASFV genotype IX in East Africa. Electronic supplementary material The online version of this article (10.1007/s11262-017-1521-4) contains supplementary material, which is available to authorized users.

Here, we report the first complete genome sequences of two strains of porcine bocavirus (JOA_011 and JOA_015) detected in Uganda and Kenya, respectively. These data will help in understanding the molecular and evolutionary characteristics of the porcine bocaviruses in this region and the development of appropriate diagnostic and control tools.