Potential routes for indirect transmission of African swine fever virus into domestic pig herds

Following its introduction into Georgia in 2007, African swine fever virus (ASFV) has become widespread on the European continent and in Asia. In many cases, the exact route of introduction into domestic pig herds cannot be determined, but most introductions are attributed to indirect virus transmission. In this review, we describe knowledge gained about different matrices that may allow introduction of the virus into pig herds. These matrices include uncooked pig meat, processed pig‐derived products, feed, matrices contaminated with the virus and blood‐feeding invertebrates. Knowledge gaps still exist, and both field studies and laboratory research are needed to enhance understanding of the risks for ASFV introductions, especially via virus‐contaminated materials, including bedding and feed, and via blood‐feeding, flying insects. Knowledge obtained from such studies can be applied to epidemiological risk assessments for the different transmission routes. Such assessments can be utilized to help predict the most effective biosecurity and control strategies.     

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

Five samples were collected from four suspected outbreaks of African swine fever in Namibia in 2018. Sequencing of the C‐terminus of the B646L gene (p72 protein), the central hypervariable region (CVR) of the B602L gene, the E183L gene (p54 protein) and the CD2v (used to determine the serogroup) was performed on DNA isolated from the samples. Phylogenetic analyses of the B646L (p72) revealed that one of the samples belonged to genotype I while the remaining samples could not be assigned to any currently known genotype. In contrast, by using the E183L gene three of the samples were shown to belong to genotype Id and only two were of unknown genotype. Based on the analysis of the partial CD2v amino acid sequences of four of the samples, one of the viruses clustered with serogroup 2 while the other three did not cluster within any of the eight known serogroups. Examination of the CVR identified three variants with 8, 18 and 24 tetrameric tandem repeat sequences. This study indicates that at least three different genetically distinct ASFV are currently present in Namibia.     

Seroprevalence of Rift valley fever in South African domestic and wild suids (1999–2016)

Rift valley fever (RVF) is a vector‐borne viral disease of domestic ruminants, camels and man, characterized by widespread abortions and neonatal deaths in animals, and flu‐like symptoms, which can progress to hepatitis and encephalitis in humans. The disease is endemic in Africa, Saudi Arabia and Yemen, and outbreaks occur after periods of high rainfall, or in environments supporting the proliferation of RVF virus (RVFV)‐infected mosquito vectors. The domestic and wild animal maintenance hosts of RVFV, which may serve as sources of virus during inter‐epidemic periods (IEPs) and contribute to occurrence of sporadic outbreaks, remain unknown, although reports indicate that the African buffalo (Syncerus caffer) may play a role. Due to the close proximity of the habitats of domestic pigs and warthogs to those of known domestic and wild ruminant RVFV maintenance hosts respectively, our study investigated their possible role in the epidemiology of RVF in South Africa by evaluating RVFV exposure and seroconversion in suids. A total of 107 warthog and 3,984 domestic pig sera from 2 and all 9 provinces of South Africa, respectively, were screened for presence of RVFV neutralizing antibodies using the virus neutralization test (VNT). Sero‐positivity rates of 1.87% (95% CI: 0.01%–6.9%) and 0.68% (95% CI: 0.49%–1.04%) were observed for warthogs and domestic pigs, respectively, but true prevalence rates, taking test sensitivity and specificity into account, were lower for both groups. There was a strong association between the results of the two groups (χ² = 0.75, p = .38), and differences in prevalence between the epidemic and IEPs were non‐significant for all suid samples tested (p > .05). This study, which provides the first evidence of probable exposure and infection of South African domestic pigs and warthogs to RVFV, indicates that further investigations are warranted, to fully clarify the role of suids in the epidemiology of RVF.     

Multilocus genotyping of Theileria parva isolates associated with a live vaccination trial in Kenya provides evidence for transmission of immunizing parasites into local tick and cattle populations

The live infection and treatment (ITM) vaccination procedure using the trivalent Muguga cocktail is increasingly being used to control East Coast fever, with potential implications for Theileria parva population genetic structure in the field. Transmission of the Kiambu V T. parva component to unvaccinated cattle has previously been described in Uganda. We monitored the T. parva carrier state in vaccinated and control animals on a farm in West Kenya where an ITM stabilate derived from the Kenyan T. parva Marikebuni stock was evaluated for field efficacy. A nested PCR‐based Marikebuni‐specific marker identified a carrier state in nine of ten vaccinated animals, detectable for a period of two years. We used 22 variable number tandem repeat (VNTR) markers to determine multilocus genotypes (MLGs) of 19 T. parva schizont‐infected lymphocyte isolates derived from cattle and field ticks. Two isolates from unimmunized cattle were identical to the Marikebuni vaccination stock. Two cattle isolates were identical to a Muguga cocktail component Kiambu V. Seven isolates from ticks exhibited MLGs that were identical to the Serengeti/Muguga vaccine stocks. Six cattle and two tick‐derived stocks exhibited unique MLGs. The data strongly suggest transmission of immunizing genotypes, from Marikebuni vaccine‐induced carrier cattle to unimmunized cattle. It is possible that genotypes similar to those in the Muguga cocktail are present in the field in Western Kenya. An alternative hypothesis is that these parasites may have originated from vaccine trial sites in Eastern Uganda. If correct, this suggests that T. parva stocks used for immunization can potentially be disseminated 125 km beyond the immediate vaccination site. Regardless of their origin, the data provide evidence that genotypes similar to those in the Muguga cocktail are circulating in the field in East Africa, alleviating concerns about dissemination of ‘alien’ T. parva germplasm through live vaccination.     

Development of a novel quantitative real‐time PCR assay with lyophilized powder reagent to detect African swine fever virus in blood samples of domestic pigs in China

African swine fever (ASF) is a devastating disease, which is causing huge economic losses in China. Therefore, it is urgent to provide a rapid, highly specific and sensitive diagnostic method for the detection of African swine fever virus (ASFV), the ASF infectious agent. In this study, a novel quantitative real‐time polymerase chain reaction (qPCR) assay with lyophilized powder reagents (LPR), targeting the major structural protein p72 gene, was established for the detection of ASFV. This assay had many advantages, such as saving time and money, good sensitivity and repeatability. The sensitivity of this assay was 100 copies/μl of ASFV plasmid templates, and the assay showed 10‐fold greater sensitivity than a qPCR assay recommended by OIE. Furthermore, specificity analysis showed that qPCR with LPR for ASFV had no cross‐reactivity with other important swine pathogens. In clinical diagnoses of 218 blood samples of domestic pigs in China, the positive rate of the diagnosis of ASFV by qPCR with the LPR and commercial kit reached 80.73% (176/218) and 76.61% (167/218) respectively. The coincidence rate between the two assays is 92.20% (201/218), and kappa value is 0.768 (p < .0001) by SPSS analysis. The overall agreement between the two assays was 95.87% (209/218). Further Pearson correlation and linear regression analysis showed a significant correlation between the two assays with an R² value of 0.9438. The entire procedure, from specimen processing to result reporting, can be completed within 2 hr. Our results demonstrated that the qPCR‐LPR assay is a good laboratory diagnostic tool for sensitive and efficient detection of ASFV.     

First detection of Theileria parva in cattle from Cameroon in the absence of the main tick vector Rhipicephalus appendiculatus

A major risk factor for the spread of livestock diseases and their vectors is the uncontrolled transboundary movement of live animals for trade and grazing. Such movements constrain effective control of tick‐transmitted pathogens, including Theileria parva. Only limited studies have been undertaken to identify ticks and tick‐borne diseases (TTBDs) affecting cattle in central African countries, including Cameroon. We hereby report the collection of baseline data on the prevalence of T. parva in Cameroon through a countrywide cross‐sectional survey, conducted in 2016, involving collection of blood samples from cattle from 63 sites across the five agro‐ecological zones (AEZs) of the country. ELISA‐based surveillance of infected cattle was performed on 479 randomly selected samples and revealed specific antibodies to T. parva in 22.7% and T. mutans in 41.1% of cattle. Screening of 1,340 representative DNA samples for the presence of T. parva identified 25 (1.86%) positives using a p104 antigen gene‐based nested PCR assay. The positives were distributed across agro‐ecological zones I, II, III and V. None of the p104 positive cattle exhibited clinical symptoms of East Coast fever (ECF). Using reverse line blot (RLB), 58 (4.3%) and 1,139 (85%) of the samples reacted with the T. parva and T. mutans oligonucleotide probes, respectively. This represents the first report of T. parva from Cameroon. Surprisingly, no Rhipicephalus appendiculatus ticks, the main vector of T. parva, were identified in a parallel study involving comprehensive morphological and molecular survey of tick species present in the country. Only two of the 25 p104 positive cattle were PCR‐positive for the CD8+ T‐cell target schizont‐expressed antigen gene Tp1. Cloning and sequencing of Tp1 amplicons revealed sequence identity with the reference T. parva Muguga. This new finding raises serious concerns of a potential spread of ECF into the central African region.     

Serological relationship between a novel ovine pestivirus and classical swine fever virus

The genus Pestivirus comprises globally distributed members of the family Flaviviridae, which cause severe losses in livestock. The most common species of the genus are bovine viral diarrhoea virus type 1 (BVDV‐1) and type 2 (BVDV‐2), classical swine fever virus (CSFV) and border disease virus (BDV). Recently, a novel ovine pestivirus was repeatedly detected in aborted lamb foetuses on a farm located in the Brescia Province (Italy). Complete genome characterization of this isolate showed that it was highly divergent from known pestivirus species and that it was genetically closely related to CSFV. The aim of this study was to determine the serological relatedness between the identified novel pestivirus and BVDV, BDV and CSFV selected strains for which homologous serum was available, by antigenic characterization performed using cross‐neutralization assays. The serological relatedness was expressed as the coefficient of antigenic similarity (R). Both field and specific antisera raised against the ovine pestivirus neutralized the CSFV reference strain Diepholz with titres significantly higher than those specific for the BDV and BVDV strains. Furthermore, the calculated R values clearly indicated that the novel ovine pestivirus is antigenically more related to CSFV than to ruminant pestiviruses, in agreement with the results of the genomic analysis. This would have severe consequences on CSFV serology in the event of a switch to porcine hosts with implications for CSFV surveillance and porcine health management.     

Unravelling animal exposure profiles of human Q fever cases in Queensland,Australia, using natural language processing

Q fever, caused by the zoonotic bacterium Coxiella burnetii, is a globally distributed emerging infectious disease. Livestock are the most important zoonotic transmission sources, yet infection in people without livestock exposure is common. Identifying potential exposure pathways is necessary to design effective interventions and aid outbreak prevention. We used natural language processing and graphical network methods to provide insights into how Q fever notifications are associated with variation in patient occupations or lifestyles. Using an 18‐year time‐series of Q fever notifications in Queensland, Australia, we used topic models to test whether compositions of patient answers to follow‐up exposure questionnaires varied between demographic groups or across geographical areas. To determine heterogeneity in possible zoonotic exposures, we explored patterns of livestock and game animal co‐exposures using Markov Random Fields models. Finally, to identify possible correlates of Q fever case severity, we modelled patient probabilities of being hospitalized as a function of particular exposures. Different demographic groups consistently reported distinct sets of exposure terms and were concentrated in different areas of the state, suggesting the presence of multiple transmission pathways. Macropod exposure was commonly reported among Q fever cases, even when exposure to cattle, sheep or goats was absent. Males, older patients and those that reported macropod exposure were more likely to be hospitalized due to Q fever infection. Our study indicates that follow‐up surveillance combined with text modelling is useful for unravelling exposure pathways in the battle to reduce Q fever incidence and associated morbidity.     

Evidence for multiple sylvatic transmission cycles during the 2016–2017 yellow fever virus outbreak,Brazil

ObjectivesSince December 2016, Brazil has experienced an unusually large outbreak of yellow fever (YF). Whether urban transmission may contribute to the extent of the outbreak is unclear. The objective of this study was to characterize YF virus (YFV) genomes and to identify spatial patterns to determine the distribution and origin of YF cases in Minas Gerais, Espírito Santo and Rio de Janeiro, the most affected Brazilian states during the current YFV outbreak.MethodsWe characterized near-complete YFV genomes from 14 human cases and two nonhuman primates (NHP), sampled from February to April 2017, retrieved epidemiologic data of cases and used a geographic information system to investigate the geospatial spread of YFV.ResultsAll YFV strains were closely related. On the basis of signature mutations, we identified two cocirculating YFV clusters. One was restricted to the hinterland of Espírito Santo state, and another formed a coastal cluster encompassing several hundred kilometers. Both clusters comprised strains from humans living in rural areas and NHP. Another NHP lineage clustered in a basal relationship. No signs of adaptation of YFV strains to human hosts were detected.ConclusionsOur data suggest sylvatic transmission during the current outbreak. Additionally, cocirculation of two distinct YFV clades occurring in humans and NHP suggests the existence of multiple sylvatic transmission cycles. Increased detection of YFV might be facilitated by raised awareness for arbovirus-mediated disease after Zika and chikungunya virus outbreaks. Further surveillance is required, as reemergence of YFV from NHPs might continue and facilitate the appearance of urban transmission cycles.