Genotypic study of Tunisian Arabian stallions

Diversity of Arabian stallions distributed throughout the territory of Tunisia has been evaluated. Seventeen microsatellite markers were used for the determination of genetic variation. A total of 95 alleles were detected in the 50 stallions studied. The number of alleles per locus ranged from 2 to 9 with an average of 5.6. The observed mean number of genetically diverse alleles (Na) was 5.6 (0.44). The mean number of expected alleles (Ne) was 3.42 (0.28). The average expected and observed heterozygosity was approximately 0.675 (0.026) and 0.593 (0.044), respectively. Principal component analysis showed the presence of 2 subpopulations in the studied sample set. These findings demonstrate the potential of microsatellites as a tool for designing and controlling animal breeds. Results show that the population under study has sufficient levels of genetic variations, which can be used as a foundation for developing plans for species conservation and long-term sustainability

Genetic analysis and phylogenetic relationships of the Barb horse through the use of microsatellites

The aim of this study was to compare genetically Moroccan (MA) and Tunisian (TN) Barb horses and toe stablish the phylogenic relation between Barb horse and other horse breeds in Morocco by using microsatellites. First, 100 Moroccan barb and 100 Tunisian Barb horses were used. Genetic variability index between and inside the populations were estimated. 133 alleles were detected in the Moroccan population and 125 in the Tunisian. The mean number of alleles was 7.29 and 7.82 respectively for the Tunisian and Moroccan barb horse. The heterozygosity was almost similar in the two groups of Barb horses (TN = 0.716 and MA = 0.714). Fst was estimated at 0.0454 and 0.0780 respectively for TN and MA Barb horses. The Gst was also estimated at 0.012 and the Nei genetic distance at 0.05. The two populations are almost genetically similar and heterogeneous. Finally, 86,5 % of horses were correctly affected to their likelihood population. Secondly, 50 Arabian horses, 50 Arabian-Barb and 50 thoroughbreds and the 200 Barb horses previously studied were used to establish the phylogenic relationships. The use of 17 microsatellites showed that the Barb horses had specific alleles and the highest heterozygosity and the highest genetic distances were obtained with thoroughbred. The two Barb horse populations were highly combined in one side of the phylogenic tree

Analyse génétique et relations phylogénétiques du cheval Barbe par l’utilisation des microsatellites

The aim of this study was to compare genetically Moroccan (MA) and Tunisian (TN) Barb horses and toe stablish the phylogenic relation between Barb horse and other horse breeds in Morocco by using microsatellites. First, 100 Moroccan barb and 100 Tunisian Barb horses were used. Genetic variability index between and inside the populations were estimated. 133 alleles were detected in the Moroccan population and 125 in the Tunisian. The mean number of alleles was 7.29 and 7.82 respectively for the Tunisian and Moroccan barb horse. The heterozygosity was almost similar in the two groups of Barb horses (TN = 0.716 and MA = 0.714). Fst was estimated at 0.0454 and 0.0780 respectively for TN and MA Barb horses. The Gst was also estimated at 0.012 and the Nei genetic distance at 0.05. The two populations are almost genetically similar and heterogeneous. Finally, 86,5 % of horses were correctly affected to their likelihood population. Secondly, 50 Arabian horses, 50 Arabian-Barb and 50 thoroughbreds and the 200 Barb horses previously studied were used to establish the phylogenic relationships. The use of 17 microsatellites showed that the Barb horses had specific alleles and the highest heterozygosity and the highest genetic distances were obtained with thoroughbred. The two Barb horse populations were highly combined in one side of the phylogenic tree. Key words: horse, barb, genetic analysis, microsatellites, genetic index, phylogenic treeCe travail s’est intéressé à la comparaison génétique entre les chevaux Barbes du Maroc et de Tunisie et à l’établissement des relations phylogénétiques entre le cheval Barbe et les autres races de chevaux existantes au Maroc par l’utilisation des microsatellites. Premièrement, 100 chevaux barbes marocains et 100 tunisiens ont été utilisés et les indices de la variabilité intra et inter-population ont été évalués. 133 allèles ont été détectés pour le Barbe marocain contre 125 pour le tunisien. Le NMA était de 7,29 et 7,82 respectivement chez le Barbe tunisien et marocain. Les taux d’hétérozygotie moyens étaient presque similaires chez les deux populations. Le Fst était de 0,0454 et 0,0780 respectivement chez le Barbe de Tunisie et du Maroc. Le Gst était très faible et la distance génétique de Nei était de 0,05. Les deux populations sont donc hétérogènes et pratiquement identiques. 86,5% des individus étudiés ont été affecté convenablement à leur population d’origine. Deuxièmement, 50 chevaux Arabe, 50 Arabe-Barbe et 50 Pur-Sang, en plus des 200 chevaux Barbes préalablement étudiés ont été utilisés. Le cheval barbe a présenté des allèles spécifiques et une forte hétérozygotie avec une distance génétique maximale avec le Pur-Sang. L’arbre phylogénétique a montré, un regroupement très significatif entre les deux populations Barbes d’un côté et les trois autres races de l’autre. Mots clés : cheval, Barbe, analyse génétique, microsatellites, indices de variabilité génétique, arbre phylogénétiqu

SARS-CoV-2 Infection in Beaver Farm, Mongolia, 2021

We report an outbreak of COVID-19 in a beaver farm in Mongolia in 2021. Genomic characterization revealed a unique combination of mutations in the SARS-CoV-2 of the infected beavers. Based on these findings, increased surveillance of farmed beavers should be encouraged

Highly pathogenic avian influenza H5N1 virus outbreak among Cape cormorants (Phalacrocorax capensis) in Namibia, 2022

ABSTRACTIn January 2022, significant mortality was observed among Cape cormorants (Phalacrocorax capensis) on the west coast of Namibia. Samples collected were shown to be positive for H5N1 avian influenza by multiplex RT-qPCR. Full genome analysis and phylogenetic analysis identified the viruses as belonging to clade 2.3.4.4b and that it clustered with similar viruses identified in Lesotho and Botswana in 2021. This is the first genomic characterization of H5N1 viruses in Namibia and has important implications for poultry disease management and wildlife conservation in the region

Comparison of the Whole-Genome Sequence of the African Swine Fever Virus from a Mongolian Wild Boar with Genotype II Viruses from Asia and Europe

African swine fever (ASF) is a highly contagious and severe viral hemorrhagic disease in domestic and wild pigs. ASF seriously affects the global swine industry as the mortality rate can reach 100% with highly virulent strains. In 2007, ASF was introduced into the Caucasus and spread to Russia and later into other European and Asian countries. This study reported the first whole-genome sequence (WGS) of the ASF virus (ASFV) that was detected in a Mongolian wild boar. This sequence was then compared to other WGS samples from Asia and Europe. Results show that the ASFV Genotype II from Mongolia is similar to the Asian Genotype II WGS. However, there were three nucleotide differences found between the Asian and European genome sequences, two of which were non-synonymous. It was also observed that the European Genotype II ASFV WGS was more diverse than that of the Asian counterparts. The study demonstrates that the ASFV Genotype II variants found in wild boars and domestic pigs are highly similar, suggesting these animals might have had direct or indirect contact, potentially through outdoor animal breeding. In conclusion, this study provides a WGS and mutation spectrum of the ASFV Genotype II WGS in Asia and Europe and thus provides important insights into the origin and spread of ASFV in Mongolia

Molecular characterization of recombinant LSDV isolates from 2022 outbreak in Indonesia through phylogenetic networks and whole-genome SNP-based analysis

Abstract Lumpy skin disease (LSD) is a transboundary viral disease of cattle and water buffaloes caused by the LSD virus, leading to high morbidity, low mortality, and a significant economic impact. Initially endemic to Africa only, LSD has spread to the Middle East, Europe, and Asia in the past decade. The most effective control strategy for LSD is the vaccination of cattle with live-attenuated LSDV vaccines. Consequently, the emergence of two groups of LSDV strains in Asian countries, one closely related to the ancient Kenyan LSDV isolates and the second made of recombinant viruses with a backbone of Neethling-vaccine and field isolates, emphasized the need for constant molecular surveillance. This current study investigated the first outbreak of LSD in Indonesia in 2022. Molecular characterization of the isolate circulating in the country based on selected LSDV-marker genes: RPO30, GPCR, EEV glycoprotein gene, and B22R, as well as whole genome analysis using several analytical tools, indicated the Indonesia LSDV isolate as a recombinant of LSDV_Neethling_vaccine_LW_1959 and LSDV_NI-2490. The analysis clustered the Indonesia_LSDV with the previously reported LSDV recombinants circulating in East and Southeast Asia, but different from the recombinant viruses in Russia and the field isolates in South-Asian countries. Additionally, this study has demonstrated alternative accurate ways of LSDV whole genome analysis and clustering of isolates, including the recombinants, instead of whole-genome phylogenetic tree analysis. These data will strengthen our understanding of the pathogens’ origin, the extent of their spread, and determination of suitable control measures required

Additional file 1 of Molecular characterization of recombinant LSDV isolates from 2022 outbreak in Indonesia through phylogenetic networks and whole-genome SNP-based analysis

Supplementary Material