Perceptions of pastoralist problems: A participatory study on animal management, disease spectrum and animal health priorities of small ruminant pastoralists in Georgia.

Small ruminants support the livelihoods of millions of poor pastoralist and sedentary households around the world. While pastoralists are generally not amongst the poorest in terms of assets, they are frequently marginalised in terms of their access to political power, health and education. This study was undertaken among pastoralist households keeping small ruminants in four regions of the country of Georgia. Small ruminants are an important cultural, social and economic asset in Georgia and are mainly managed in a transhumant pastoralist system. Georgia suffered its first, and so far only outbreak of peste des petits ruminants (PPR) in 2016. This qualitative interview study was designed to acquire contextual understanding of local small ruminant husbandry and the livelihood situations of the participating pastoralists, and to detect historical, unreported PPR outbreaks. Focus group discussions comprising participatory epidemiology tools and other forms of interviews were used to explore small ruminant management, disease spectrum and management, and animal health priorities. The participants had experienced a wide variety of animal health constraints, with intestinal worms, braxy, piroplasmosis, pasture-related problems, predators and lameness emerging as priorities. No historic, unreported PPR outbreak was detected in this study, and PPR was not a priority for participants. Instead, the day-to-day reality of animal health for the pastoralists was characterised by co-infections of mainly endemic pathogens, and problems related to other challenges such as access to land, feed and genetic resources. The rationale behind the participants' prioritisation of animal health problems was supported by the need to pay extra attention to animals in order to avoid risk factors, keep animals healthy and minimise the negative impact of diseases or management problems; the various epidemiological and clinical parameters of the prioritised diseases; the economic impact of the specific problems and the zoonotic potential of diseases and predation. Even within regions, and within seemingly socially and culturally homogenous groups, there were important local differences in the problems faced by pastoralists that affect their livestock management. This study underlines the importance of a contextualised understanding of the local disease panorama and complexities in the livelihood situations of rural people when designing actions to improve animal health in general or, more specifically, passive surveillance as well as prevention or control measures. Finally, it is concluded that to achieve such an understanding, there is a need for participatory, scoping-style studies that specifically acknowledge diversity and power relations.

Intra-epidemic genome variation in highly pathogenic African swine fever virus (ASFV) from the country of Georgia.

BACKGROUND: African swine fever virus (ASFV) causes an acute hemorrhagic infection in suids with a mortality rate of up to 100%. No vaccine is available and the potential for catastrophic disease in Europe remains elevated due to the ongoing ASF epidemic in Russia and Baltic countries. To date, intra-epidemic whole-genome variation for ASFV has not been reported. To provide a more comprehensive baseline for genetic variation early in the ASF outbreak, we sequenced two Georgian ASFV samples, G-2008/1 and G-2008/2, derived from domestic porcine blood collected in 2008. METHODS: Genomic DNA was extracted directly from low-volume ASFV PCR-positive porcine blood samples and subjected to next generation sequencing on the Illumina Miseq platform. De novo and mapped sequence assemblies were performed using CLCBio software. Genomic illustrations, sequence alignments and assembly figures were generated using Geneious v10.2.4. Sequence repeat architecture was analyzed using DNASTAR GeneQuest 14.1.0. RESULTS: The G-2008/1 and G-2008/2 genomes were distinguished from each other by coding changes in seven genes, including MGF 110-1 L, X69R, MGF 505-10R, EP364R, H233R, E199L, and MGF 360-21R in addition to eight homopolymer tract variations. The 2008/2 genome possessed a novel allele state at a previously undescribed intergenic repeat locus between genes C315R and C147L. The C315R/C147L locus represents the earliest observed variable repeat sequence polymorphism reported among isolates from this epidemic. No sequence variation was observed in conventional ASFV subtyping markers. The two genomes exhibited complete collinearity and identical gene content with the Georgia 2007/1 reference genome. Approximately 56 unique homopolymer A/T-tract variations were identified that were unique to the Georgia 2007/1 genome. In both 2008 genomes, within-sample sequence read heterogeneity was evident at six homopolymeric G/C-tracts confined to the known hypervariable ~ 7 kb region in the left terminal region of the genome. CONCLUSIONS: This is the first intra-epidemic comparative genomic analysis reported for ASFV and provides insight into the intra-epidemic microevolution of ASFV. The genomes reported here, in addition to the G-2007/1 genome, provide an early baseline for future genome-level comparisons and epidemiological tracing efforts.