Background: Bovine trypanosomosis transmitted by tsetse flies is a major constraint to cattle health and productivity in all sub-Saharan countries, including Uganda. The objectives of this study were to determine the prevalence of bovine trypanosomosis and identify its associated risk factors and the species of trypanosomes associated with the disease. Methodology: A cross-sectional study was conducted around Murchison Falls National Park, Uganda from January 2020 to April 2020. Trypanosomes were detected in blood samples by PCR analysis targeting the internal transcribed spacer 1 (ITS-PCR assays), and trypanosomes in positive blood samples were sequenced. Results: Of 460 blood samples collected and tested, 136 (29.6%) were positive for trypanosome infections and 324 (70.4%) were negative. The overall trypanosome prevalence was 29.6% (95% confidence interval 25.4–33.8%), attributed to three trypanosome species. Of these three species, Trypanosoma vivax was the most prevalent (n = 130, 28.3%) while the others were detected as mixed infections: T. vivax + Trypanosomacongolense (n = 2, 0.4%) and T. vivax + Trypanosomaevansi (n = 1, 0.2%). There were significant differences in trypanosome prevalence according to sex (χ² = 62, df = 1, P < 0.05), age (χ² = 6.28, df = 2, P = 0.0043) and cattle breed (χ² = 10.61, df = 1, P = 0.001). Conclusions: Trypanosomosis remains a major limitation to cattle production around Murchison Falls National Park and interventions are urgently needed. In our study, the prevalence of trypanosome infections was high, with T. vivax identified as the most prevalent species. Age, sex and breed of cattle were risk factors for trypanosome infection. Graphical

Blood samples were collected from pigs at six abattoirs in the Kampala, Uganda metropolitan area from May 2021 through June 2022, and tested for African swine fever virus. Thirty-one samples with cycle threshold values < 26 from pigs with different geographic origins, clinical and pathologic signs, and Ornithodoros moubata exposure underwent whole genome sequencing. The p72 gene was used to genotype the isolates, and all were found to be genotype IX; whole genome sequences to previous genotype IX isolates confirmed their similarity. Six of the isolates had enough coverage to evaluate single nucleotide polymorphisms (SNPs). Five of the isolates differed from historic regional isolates, but had similar SNPs to one another, and the sixth isolate also differed from historic regional isolates, but also differed from the other five isolates, even though they are all genotype IX. Whole genome sequencing data provide additional detail on viral evolution that can be useful for molecular epidemiology, and understanding the impact of changes in genes to disease phenotypes, and may be needed for vaccine targeting should a commercial vaccine become available. More sequencing of African swine fever virus isolates is needed in Uganda to understand how and when the virus is changing.

Use of meat juice and muscle swabs at slaughterhouses may provide an easy-to-collect sample for African swine fever (ASF) surveillance. Meat juice has been experimentally shown to be a reliable sample for the detection of ASF virus (ASFV). We compared the detection of ASFV nucleic acid from diaphragm meat juice, diaphragm muscle swab, spleen, and spleen swabs from pigs with signs of ASFV infection at slaughterhouses around Kampala, Uganda. Pigs with ≥2 clinical or pathology signs at the time of slaughter had a spleen sample, spleen swab, diaphragm muscle sample, and diaphragm muscle swab collected. Meat juice was collected from muscle samples through a freeze–thaw cycle. Each sample was tested individually, and 72 spleen, meat juice, and muscle swab sample pools of 4 negative and 1 positive sample were tested, as well. Standard operating procedures from the USDA–Foreign Animal Disease Diagnostic Laboratory for viral DNA extraction and real-time PCR (rtPCR) were used. Of the 493 pigs evaluated, we classified as positive 357 (72.4%) diaphragm meat juice samples, 218 (44.2%) diaphragm muscle swabs, 247 (50.1%) spleen samples, and 241 (48.9%) spleen swabs. All spleen sample pools were positive (72 of 72; 100%), as were 71 of 72 (98.6%) meat juice pools and 67 of 72 (93.1%) muscle swab pools. Meat juice samples provided a reliable sample type for the detection by rtPCR of ASFV in pigs with natural infections.

Domestic cattle in Africa can be categorized as either taurine ( Bos taurus ) or indicine ( Bos indicus ) based on their domestication histories from the extinct aurochs ( Bos primigenius ). Close to 150 breeds of indigenous cattle are estimated to exist in Africa and have a complex mixture of B. taurus and B. indicus ancestries. Native cattle in Uganda fall into three broad categories: the Sanga, East African Shorthorn Zebu, and Zenga. There is limited information about the genetics of Ugandan indigenous cattle, despite their representation of nearly 80% of the national herd. In the present study, we describe the genetic diversity and population structure of five native breeds using whole genome sequences of 95 animals. For a comparative context, we included published whole genome sequences of 97 animals in the analysis. Our findings indicate a clear distinction between Zebu, Sanga, and Zenga breeds, with elevated inbreeding and lower genetic diversity levels among the Ugandan breeds. We also observed an introgression of European genetic resources into Ugandan native cattle breeds. Notably, our results suggest existence of two subpopulations within the Nganda breed, a finding that has implications on the conservation efforts of native animal genetic resources. The findings of this study show that indigenous cattle genetic resources in the country are threatened by admixture with imported genetic material and underscore the need for targeted efforts to characterize and conserve them before they are lost to crossbreeding and breed substitution.

Indigenous cattle account for approximately 80% of Uganda’s cattle population. These animals are well adapted to the country’s ten agroecological zones and are mainly kept under pastoral and agropastoral systems. Unlike commercial breeds, they thrive on low-quality feeds, while tolerating major tropical diseases and parasites including tsetse flies, ticks, and vector-borne infections. Whole-genome sequence (WGS) analysis offers opportunities to uncover genomic regions underlying these adaptations and to trace the genetic footprints of long-term breeding decisions taken by cattle keepers. In this study, WGS data from 95 animals representing six indigenous cattle populations (Ankole, Karamojong, Nganda10, Nganda17, Nkedi, and Ntuku) were analyzed to identify genomic regions under putative selection. Two complementary approaches were applied: enumeration of the µ-statistic in RAiSD and runs of homozygosity (ROH) analysis. RAiSD identified population-level signals, while conserved ROH regions were defined using breed-specific SNP-incidence thresholds. The two methods identified 803 and 49 candidate genes respectively. The top genes identified included SLC37A1 (BTA1), CHCHD3 (BTA4), and RAB3GAP1 (BTA2) detected by RAiSD, and IL26 (BTA5), FBXL7 (BTA20), and HSPA9 (BTA7) contained in ROH. Furthermore, the regions harbored 107 novel genes (92 detected by RAiSD and 15 by ROH), corresponding to 255 quantitative trait loci. The identified genes under putative selection are associated with economically important traits including adaptation to tropical environments, resistance to parasites and diseases, and other farmer-preferred characteristics. These findings provide insights into the genetic basis of adaptation, selection and production in Ugandan indigenous cattle, supporting conservation and breeding strategies to enhance resilience and productivity.

Background: Diagnostic tests and knowledge of their diagnostic accuracies are important for animal trypanosomosis surveillance and treatment. Methodology: : A cross-sectional study was conducted in November 2021 to compare the performance of rapid diagnostic test (RDT) and PCR-based assay for the detection of trypanosome infections. Random sampling and probability proportional to size sampling were used to sample study households and animals from the sampled household respectively. Animals were screened for the presence of trypanosomes using both tests. A total of 100 cattle (52 from Apac and 48 from Kiryandongo districts) were included in the study. The percentage of positive tests, sensitivity, and specificity of the tests using mini PCR as a reference were computed. Cohen’s kappa statistics was computed to assess how well the rapid diagnostic test agrees with the mini PCR. McNemar’s statistic assessed if the proportion of positive tests identified by mini PCR significantly differed from that identified by the rapid diagnostic test. Results: The mini PCR test detected 31.2% Trypanosome spp positive samples in Kiryandongo while it detected only 5.7% positive samples in Apac district. The rapid diagnostic test (RDT) analysis detected 91.6% Trypanosome spp positive samples in Kiryandongo district and only 46.1% in Apac district. T. congolense was the most common Trypanosoma species identified in Apac (36.5%) and Kiryandongo (47.9%) by the RDT. The percentage of each of the Trypanosome species (T.vivax, T.congolense, and mixed infection of T.vivax and T. congolense) detected by RDT differed significantly (p < 0.001) between the two districts. The RDT had a high sensitivity of 94.4% (95% Confidence Interval (CI): 72.7–99.9) but a very low specificity of 36.6% (95% CI: 26.2–48.0). The kappa test showed evidence of only a slight agreement (kappa = 0.1547, Accuracy = 0.48 (95% Confidence Interval (CI): 0.379,0.5822) between the two tests. The observed agreement between the tests was 47% while the expected agreement was 37.84%. Conclusion: This study found high sensitivity but low specificity of RDT using mini PCR as a reference.