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The diversity in genome resources is fundamental to designing genomic strategies for local breed improvement and utilisation. These resources also support gene discovery and enhance our understanding of the mechanisms of resilience with applications beyond local breeds. Here, we report the genome sequences of 555 cattle (208 of which comprise new data) and high-density (HD) array genotyping of 1,082 samples (537 new samples) from indigenous African cattle populations. The new sequences have an average genome coverage of ~30X, three times higher than the average (~10X) of the over 300 sequences already in the public domain. Following variant quality checks, we identified approximately 32.3 million sequence variants and 661,943 HD autosomal variants mapped to the Bos taurus reference genome (ARS-UCD1.2). The new datasets were generated as part of the Centre for Tropical Livestock Genetics and Health (CTLGH) Genomic Reference Resource for African Cattle (GRRFAC) initiative, which aspires to facilitate the generation of this livestock resource and hopes for its utilisation for complete indigenous breed characterisation and sustainable global livestock improvement.

Theileria parva is the causative agent of East Coast fever and Corridor disease, which are fatal, economically important diseases of cattle in eastern, central and southern Africa. Improved methods of control of the diseases are urgently required. The parasite transforms host lymphocytes, resulting in a rapid, clonal expansion of infected cells. Resistance to the disease has long been reported in cattle from T. parva -endemic areas. We reveal here that first- and second-generation descendants of a single Bos indicus bull survived severe challenge with T. parva , (overall survival rate 57.3% compared to 8.7% for unrelated animals) in a series of five field studies. Tolerant cattle displayed a delayed and less severe parasitosis and febrile response than unrelated animals. The in vitro proliferation of cells from surviving cattle was much reduced compared to those from animals that succumbed to infection. Additionally, some pro-inflammatory cytokines such as IL1β, IL6, TNFα or TGFβ which are usually strongly expressed in susceptible animals and are known to regulate cell growth or motility, remain low in tolerant animals. This correlates with the reduced proliferation and less severe clinical reactions observed in tolerant cattle. The results show for the first time that the inherited tolerance to T. parva is associated with decreased proliferation of infected lymphocytes. The results are discussed in terms of whether the reduced proliferation is the result of a perturbation of the transformation mechanism induced in infected cells or is due to an innate immune response present in the tolerant cattle.

Gastrointestinal nematodes (GIN) are of major concern in dairy farming, particularly in smallholder systems, because of their impact on the health of the calves and later on their productivity. These infections often occur as co-infections, which can complicate their prevention and treatment. The aim of this study was to conduct fecal egg counts (FEC), genetically identify GIN species, assess species diversity, and identify associated risk factors for GIN infections in dairy calves. Fecal samples were collected from 532 dairy calves across 289 small holder dairy farms. Species identification was achieved through deep amplicon sequencing of the Internal Transcribed Spacer-2 rDNA locus (ITS-2) of first-stage larvae (L1). The mean eggs per gram (EPG) was 62.0 ± 93.0. Most of the calves 64.2% had low-intensity infections (<50 EPG), 28.6% had medium-intensity infections (50–200 EPG), and 7.2% had high-intensity infections (>200 EPG). Next Generation Sequencing analysis identified nine GIN species, with Cooperia punctata (27.8%), Haemonchus placei (26.3%), and Haemonchus contortus (23.6%) being the most prevalent. Co-infections were common, accounting for 69.5% of all infections, with two (40.1%), three (26.9%), and four-species combinations (19.8%) predominating. Male calves showed a significant association with both increased FEC and smaller heart girth, while FEC decreased with age. H. placei and C. punctata were associated with increased FEC, whereas Ostertagia ostertagi (14.5%) and Trichostrongylus colubriformis (8.0%) were associated with decreased heart girth. Calves managed under pasture systems had higher odds of co-infection. This study reveals that GIN infections are highly prevalent in dairy calves, with co-infections being common, and that GIN burden is significantly influenced by calf age, sex, and management system. The Nemabiome tool offers a promising approach to assessing GIN burden and guiding the selection of anthelmintic protocols as part of sustainable farming strategies in tropical regions.

Smallholder pig farming is an important economic activity for many poor, rural communities in developing countries. Porcine cysticercosis is a growing public health risk in countries where pig rearing is popular. A sanitation-based intervention to reduce the prevalence of open defecation was completed in Busia County, Kenya in 2016. We capitalized on this third party intervention to evaluate its impact on porcine cysticercosis prevalence. We conducted a comparative cross-sectional survey from August through to September 2021. Household selection was done using multistage sampling. Household questionnaire data on pig production, transmission, risk factors and awareness of porcine cysticercosis were collected from 251 households. Lingual palpation was used to test for cysticerci in 370 pigs while serum was tested for circulating antigen using Ag-ELISA. We compared results of our survey to an effective baseline, which was a near equivalent cross sectional survey conducted in 2012 before the third party sanitary intervention was established. The difference in prevalence was measured using Chi-square tests. Multivariable logistic regression analysis was used to identify risk factors for lingual cysts in pigs. The prevalence of palpable lingual cysts was estimated to be 3.8% (95% CI 2.3-6.3%) (14/370). This was 6% (95% CI 0.8-13.9%; -value 0.0178) lower than the prevalence reported in the pre-implementation period of 9.7% (95% CI: 4.5-17.6%). Circulating antigen was detected in 2 samples (0.54%, 95% CI: 0.2-1.9). Latrine coverage was 86% (95% CI: 81-90%), which was 11% (95% CI: 4.8-16.8%;  < 0.001) higher than the pre-implementation period coverage of 75% (95% CI: 71-79%). There was reduced prevalence of lingual cysts in pigs from households that had a latrine (OR = 0.14; 95% CI: 0.05-0.43;  < 0.001) and where pigs were confined or tethered (OR = 0.27; 95% CI: 0.07-1.02;  = 0.053). There was a reduction in the prevalence of porcine cysticercosis in Busia County over the study period from 2012 to 2021. This was not a trial design so we are unable to directly link the decline to a specific cause, but the data are consistent with previous research indicating that improved sanitation reduces porcine cysticercosis. Programs for controlling porcine cysticercosis should include a focus on sanitation in addition to other integrated One Health approaches.

Corridor disease (CD) is a fatal condition of cattle caused by buffalo-derived Theileria parva . Unlike the related condition, East Coast fever, which results from infection with cattle-derived T. parva , CD has not been extensively studied. We describe in detail the clinical and laboratory findings in cattle naturally infected with buffalo-derived T. parva . Forty-six cattle were exposed to buffalo-derived T. parva under field conditions at the Ol Pejeta Conservancy, Kenya, between 2013 and 2018. The first signs of disease observed in all animals were nasal discharge (mean day of onset was 9 days post-exposure), enlarged lymph nodes (10 days post-exposure), and pyrexia (13.7 days post-exposure). Coughing and labored breathing were observed in more than 50% of animals (14 days post-exposure). Less commonly observed signs, corneal edema (22%) and diarrhea (11%), were observed later in the disease progression (19 days post-exposure). All infections were considered clinically severe, and 42 animals succumbed to infection. The mean time to death across all studies was 18.4 days. The mean time from onset of clinical signs to death was 9 days and from pyrexia to death was 4.8 days, indicating a relatively short duration of clinical illness. There were significant relationships between days to death and the days to first temperature (chi 2 = 4.00, p = 0.046), and days to peak temperature (chi 2 = 25.81, p = 0.001), animals with earlier onset pyrexia died sooner. These clinical indicators may be useful for assessing the severity of disease in the future. All infections were confirmed by the presence of macroschizonts in lymph node biopsies (mean time to parasitosis was 11 days). Piroplasms were detected in the blood of two animals (4%) and 20 (43%) animals seroconverted. In this study, we demonstrate the successful approach to an experimental field study for CD in cattle. We also describe the clinical progression of CD in naturally infected cattle, including the onset and severity of clinical signs and pathology. Laboratory diagnoses based on examination of blood samples are unreliable, and alternatives may not be available to cattle keepers. The rapid development of CD requires recognition of the clinical signs, which may be useful for early diagnosis of the disease and effective intervention for affected animals.

East Coast fever, a tick-borne cattle disease caused by the Theileria parva parasite, is among the biggest natural killers of cattle in East Africa, leading to over 1 million deaths annually. Here we report on the genetic analysis of a cohort of Bos indicus (Boran) cattle demonstrating heritable tolerance to infection with T . parva ( h 2 = 0.65, s.e. 0.57). Through a linkage analysis we identify a 6 Mb genomic region on bovine chromosome 15 that is significantly associated with survival outcome following T . parva exposure. Testing this locus in an independent cohort of animals replicates this association with survival following T . parva infection. A stop gained variant in a paralogue of the FAF1 gene in this region was found to be highly associated with survival across both related and unrelated animals, with only one of the 20 homozygote carriers (T/T) of this change succumbing to the disease in contrast to 44 out of 97 animals homozygote for the reference allele (C/C). Consequently, we present a genetic locus linked to tolerance of one of Africa’s most important cattle diseases, raising the promise of marker-assisted selection for cattle that are less susceptible to infection by T . parva .

East Coast fever, a tick-borne cattle disease caused by the Theileria parva parasite, is among the biggest natural killers of cattle in East Africa, leading to over 1 million deaths annually. Here we report on the genetic analysis of a cohort of Bos indicus (Boran) cattle demonstrating heritable tolerance to infection with T. parva (h2 = 0.65, s.e. 0.57). Through a linkage analysis we identify a 6 Mb genomic region on bovine chromosome 15 that is significantly associated with survival outcome following T. parva exposure. Testing this locus in an independent cohort of animals replicates this association with survival following T. parva infection. A stop gained variant in a paralogue of the FAF1 gene in this region was found to be highly associated with survival across both related and unrelated animals, with only one of the 20 homozygote carriers (T/T) of this change succumbing to the disease in contrast to 44 out of 97 animals homozygote for the reference allele (C/C). Consequently, we present a genetic locus linked to tolerance of one of Africa's most important cattle diseases, raising the promise of marker-assisted selection for cattle that are less susceptible to infection by T. parva.

East Coast fever, a tick-borne cattle disease caused by the Theileria parva parasite, is among the biggest natural killers of cattle in East Africa, leading to over 1 million deaths annually. Here we report on the genetic analysis of a cohort of Boran cattle demonstrating heritable tolerance to infection by T. parva (h2 = 0.65, s.e. 0.57). Through a linkage analysis we identify a 6 Mb genomic region on Bos taurus chromosome 15 that is significantly associated with survival outcome following T. parva exposure. Testing this locus in an independent cohort of animals replicates this association with survival following T. parva infection. A stop gained polymorphism in this region was found to be highly associated with survival across both related and unrelated animals, with only one of the 20 homozygote carriers (T/T) of this change succumbing to the disease in contrast to 44 out of 97 animals homozygote for the reference allele (C/C). Consequently, we present a genetic locus linked to tolerance of one of Africa's most important cattle diseases, raising the promise of marker-assisted selection for cattle that are less susceptible to infection by T. parva. Competing Interest Statement The Centre for Tropical Livestock Genetics and Health (CTLGH) has filed a patent application regarding the use of this locus in improving cattle through methods such as marker assisted breeding. Footnotes * Relative risk updated. Covariates used in fitting model on IDEAL data clarified. * https://doi.org/10.7488/ds/2985

With the increasing concerns on the impact of cement production on the environment and the need to protect the environment, the use of mineral additives as cementitious material to partially substitute cement is being considered as an effective option. One of such material is fired clay brick which can be sourced as generated waste from clay brick industry. This has an added advantage of reducing industrial waste and preserving the natural resources. The experimental objective of this study is to examine the possibility of utilizing clay brick waste as partial replacement for Portland cement in concrete. The clay brick was finely ground into powder size, and after grinding, the morphological characterization of the powder materials was carried out using scanning electron microscopy (SEM). Moreover, the chemical composition of the brick material was determined using X-ray fluorescence (XRF). Laboratory tests were carried out to determine the workability, split tensile and compressive strength properties of the concrete with 0%, 10%, 20%, 30% and 40% partial replacement of cement with ground clay brick (CB). From the test results, the chemical composition of the brick powder meets the standard requirements for pozzolanic material, with the SEM revealing an amorphous solid mass. The workability of the concrete reduces with increase in brick powder content. A significant improvement of the split tensile and compressive strength of the concrete was achieved at 10% cement replacement, after which a decrease in strength with increasing ground clay brick content was recorded. The use of ground clay brick of not more than 15% was recommended for concrete production.