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African Swine Fever, the Sus scrofa evolutionary genomic response

Periodic Reporting for period 1 - ASF_SwineResistance (African Swine Fever, the Sus scrofa evolutionary genomic response)

Reporting period: 2015-05-01 to 2017-04-30

African Swine Fever (ASF) is a notifiable devastating hemorrhagic fever, caused by a virus, with mortality rates up to 100% in pigs. It affects all members of the Suidae family and is one of the most important pig diseases due to its severe socio-economic consequences for affected countries, the difficulty of preventing spread across country boundaries, and the lack of vaccine or therapeutic control measures. The transmission cycle can involve different hosts and the virus can survive for several months in the environment or in pig products. This is particularly important as, although the virus is not a threat for humans, direct transmission between pigs or consumption of infected wastes are considered the most common and efficient transmission routes.
The virus is endemic in several African countries, where the presence of resistant Suids (e.g. Potamochoerus larvatus) contributes to the cycle, and in Sardinia since 1978. In 2007 it reached Georgia and started spreading through the Caucasian area, subsequently reaching Russia and afterwards the Baltic countries and Europe. ASF can cause important economic losses and can create health related problems in forested areas due to the presence of wild boar carcases killed by the virus. Additionally, the possibility of outbreaks in a high mobile species, like the wild boar, might increase the possibility of spread among countries. Although this is not going to affect industrial farms, it could create problems to small, backyard and organic farms, as well as for hunting associations that integrate their incomes by selling the meat, with negative impact on local communities economy.
This project aimed at using genome-wide DNA technologies to understand if there is anything in the wild boar and domestic pig genome that might help counteracting the infection or that could be targeted to develop a cure. Additionally, we wanted to assess the hybridization rate between the domestic pig and the wild boar to identify possible transmission routes in pig diseases (not only ASF). Our results are not optimistic concerning the development of genetic-based veterinary treatment, as we found statistically significant difference between the genomes of healthy and infected individuals. However, the analysis of hybridization levels detected the presence of a few areas at higher risk, where we could concentrate efforts (by for e.g. building fences around outdoor farms) to prevent the spread of diseases. This is particularly important as small local pig farms, due to their lower biosecurity measures, are more at risk and this might have a heavy impact on local economies that rely on backyard farming or selling wild boar meat for their income.
During the project I established numerous collaborations, across two continents (Africa and Europe), that made it possible to acquire samples and that are now contributing to the analysis and interpretation of data. The presence of genomic regions under selection for ASF was initially investigated with a Genome Wide Association Study (GWAS) which showed no difference between healthy and infected individuals, concordantly with the variability in immune-related genes. However, we are now performing an additional analysis based on haplotypes, instead of single loci to further address this topic.
Hybridization was studied using about 300 samples of domestic pigs, from 23 breeds, and a similar number of wild boars, from 24 European and 3 Near Eastern countries. Our results showed variable levels of hybridization though Europe. Overall the two populations are well differentiated, but in a few geographic areas hybridization can reach 100% in frequency. These areas usually are characterised by the presence of outdoor farming. We thus suggest to improve the fencing around these farms, to prevent both hybridization and disease spread.
These results were presented at international conferences and within a Cost action aiming at dealing with ASF and a scientific publication is now being prepared. At the conferences our audience included people from all over European and Africa, with different expertise such as veterinarians, wild boar experts, forestry managers, virologist, policy makers and managers. Additionally, thanks to TV coverage, the main points of some of the conferences were made available to the broad public. However, details on the project are also open to the public through my webpage.
Additionally, some of the research lines have been published in scientific journals. The preparation study on of the genome of an isolated, although managed, island population was published in Heredity in 2016. This paper on the Sardinian wild boar highlighted low levels of hybridization but high differentiation from other wild boar populations. We observed that the closer population is the Italian wild boar, in accordance with other molecular markers, and the most differentiated is the domestic pig. Additionally, despite introgression from both domestic and continental wild boar, the Sardinian population still shows signatures of evolutionary differentiation.
A study on hybridization levels focusing on two autosomal genes, the MC1R and the NR6A1, that underwent strong human selection during domestication processes was also published in 2016 in Mammalian Biology. MC1R codes for fur colour, while NR6A1 is involved in the development of the number of vertebrae. Both genes present different variants between the domestic pig and the wild boar, that usually have a single fixed allele (wild type). We sampled wild boar throughout Europe and observed that most of the analysed wild boars carried only the wild type allele, however, in 6% cases animals showed signs of introgression from the domestic counterpart with each marker. Considered together the two genes identified 11% of hybrids in the overall sample.
Finally, at the beginning of 2017 we published in Behavioural Processes a study on the behaviour of and towards hybrids in the wild. With this aim we considered movies captured by camera traps in Tuscany and analysed the behaviour of animals belonging to the same social unit. This is particularly important for a species, like the wild boar, where social bonds and cooperation are paramount. In this case we classified as hybrids individuals that had, partly or completely, the aspect of a domestic pig. What we observed is that animals that look like pigs were the last ones in their social unit and were often harassed by their fellows (while no aggression was recorded among animals that looked like wild boars). Our hypothesis is that the lack of camouflage might put the whole group at risk of predation.
The mapping of hybridization levels across European countries we performed is now discussed among wild boar managers from different European countries. This information will be implemented in plans aimed at controlling the population, possibly decreasing human-wildlife conflict in some areas and thus the compensation needed to deal with wildlife-caused damages.
Additionally, this information will be included in the development of contingency plans for disease spread. Focusing efforts in areas at higher risk, or where human behaviours increase the chance of contagion, will increase the efficacy of these plans, while reducing costs at the same time.
Wild boar