ILRI articles in journals

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The genetic structure and diversity of smallholder dairy cattle in Rwanda
(Journal Article, 2025-05-27) Opoola, O.; Shumbusho, F.; Rwamuhizi, I.; Houaga, I.; Harvey, D.; Hambrook, D.; Watson, K.; Chagunda, M.G.G.; Mrode, Raphael A.; Djikeng, Appolinaire
Previous genomic characterisation of Rwanda dairy cattle predominantly focused on the One Cow per Poor Family (locally called “Girinka”) programme. However, smallholder farmers in Rwanda have benefited from other livestock initiatives and development programmes. Capturing and documenting the genetic diversity, is critical in part as a key contribution to genomic resource required to support dairy development in Rwanda. A total of 2,229 crossbred animals located in all dairy-producing regions of Rwanda were sampled. For each animal, a hair sample was collected and genotyped by using the Geneseek Genomic Profiler (GGP, Neogen Geneseek®) Bovine 50 K (n = 1,917) and GGP Bovine 100 K arrays (n = 312). The combined dataset was subject to quality control, data curation for use in population genetics and genomic analyses. To assess the genetic structure and diversity of the current population, key analyses for population structure were applied: Principal Component Analysis (PCA), population structure and diversity, admixture analysis, measures of heterozygosity, runs of homozygosity (ROH) and minor allelic frequency (MAF). A dataset of global dairy population of European taurine, African indicus and African taurus (n = 250) was used as reference. Results showed that Rwanda cattle population is highly admixed of diverse pure and crossbred animals with average MAF of 33% (standard error; se = 0.001) with proportion of foreign high yielding (taurine) dairy breeds of Jersey Island (18%); 12% non-Island Jersey and 42% Holstein-Friesian ancestries. Two African Bos taurus and five Bos indicus breeds contributed 28% of their genetics. Genetic distances were highest in Gir and N’dama (0.29); and Nelore and N’dama (0.29). There were 1,331 ROH regions and average heterozygosity were high for Rwanda cattle (0.41 se = 0.001). Asides well-established genes in cattle, we found evidence for a variety of novel and less-known genes under selection to be associated with fertility, milk production, innate immunity and environmental adaptation. This observed diversity offers opportunity to decipher the presence and/or lack of genetic variations to initiate short- and long-term breed improvement programmes for adaptation traits, disease resistance, heat tolerance, productivity and profitability of smallholder dairy systems in Rwanda.
Environmental risk factors associated with community diarrheal disease in Ethiopia
(Journal Article, 2025-05-27) LaPolt, D.; Smith, S.; Gazu, Lina; Alonso, Silvia; Teshale, A.M.; Azmeraye, B.M.; Ayana, G.M.; Angaw, D.A.; Degefaw, D.; Garsow, A.V.; Beczkiewicz, A.; Yimer, G.; Krakowski, M.J.; Scharff, R.; Seyoum, E.T.; Kowalcyk, B.
Background: Diarrhea is a major contributor to mortality in sub-Saharan Africa, where access to improved sanitation and clean water is limited. Identifying factors associated with diarrhea across geographical regions and age groups can inform resource allocation toward water infrastructure, healthcare, and disease mitigation. The objective of this study was to identify environmental risk factors associated with diarrhea in the general population across multiple communities in Ethiopia. Methods: A prospective cross-sectional study was conducted in three regions in Ethiopia from October 2021-October 2022. REDCAP mobile app was used to collect data during face-to-face interviews using a structured, pretested questionnaire. Descriptive statistics characterized household environmental exposures. Univariate and multivariable logistic regression were used to identify factors associated with diarrhea. Results: A total of 2,436 households participated in the study. Of these, 10.3% of households reported at least one case of diarrhea during the previous four weeks. Household animal ownership varied by site, with Addis Ababa reporting the lowest animal ownership and Harar reporting the highest ownership. Across all sites, pit latrines without covers were the most common sanitation facility. Water piped to yard was the most frequent source of drinking water and most households did not use treated water (boiled/filtered) when handling food. No environmental factors were associated with diarrhea in Addis Ababa. In Gondar, drinking water from unprotected wells was associated with increased odds of diarrhea [COR:4.81(95%CI:2.03,11.43)]. Dry season was associated with decreased odds of diarrhea compared to short [COR:0.42(95%CI:0.24,0.75)] and long rains seasons [COR:0.55(95%CI: 0.34,0.88)]. In Harar, drinking water from communal taps was associated with increased odds of diarrhea [COR:2.02(95%CI:1.32,3.09)]. Conclusion: Multiple environmental factors for diarrhea were identified. Given the variation in factors by site, strategies for intervention and management should be community-specific. These factors can be managed through improved water treatment, sanitation practices, and educational programs focused on proper hygiene. Efforts to manage these factors can potentially reduce the burden of diarrheal diseases.
Spatial and temporal analysis of Rift Valley fever outbreaks in livestock in Uganda: a retrospective study from 2013 to 2022
(Journal Article, 2025-05-26) Arinaitwe, E.; Atuhaire, D.K.; Hasahya, Emmanuel; Nakanjako, G.K.; Mwebe, R.; Nizeyimana, G.; Afayoa, M.; Mwiine, F.N.; Erume, J.
Background: Rift Valley fever (RVF) is a zoonotic disease caused by the Rift Valley fever virus (RVFV), primarily affecting livestock and transmitted by Aedes mosquitoes. First detected in Kenya in 1930, RVF has since spread across Africa, including Uganda, and to the Arabian Peninsula. Uganda reported its first human cases of RVF in 1968, with sporadic outbreaks continuing since the significant outbreak in 2016, particularly in regions with high livestock populations. Although RVFV was detected in mosquitoes in Uganda as early as 1944, the spatial and temporal distribution of RVF outbreaks has not been thoroughly documented. This study aimed to analyze trends in RVF outbreaks across Uganda from 2013 to 2022 to provide insights for effective control measures. A retrospective study was conducted utilizing archived RVF data from NADDEC, along with rainfall and temperature data from the Uganda Meteorological Centre. Maps were generated using QGIS software to illustrate the spatial distribution of RVF outbreaks. The distribution and trends were analyzed using the R programming language. Results: During the study period, RVF outbreaks were reported in 74.1% of districts surveyed, representing 27.2% of all districts nationwide. The overall RVF seropositivity among tested animals was found to be 13.02% [95% CI: 12.4–13.7%], with bovine exhibiting the highest RVF seropositivity among the commonly raised species, such as cattle, goats and sheep. The year 2017 recorded the highest RVF seropositivity at 19.6%. Notably, the central region had the highest RVF seropositivity at 17.7% [95% CI: 15.8–19.7%] while the eastern region recorded the lowest at 4.6%. Conclusion: This analysis provides crucial insights into the spatial and temporal patterns of RVF outbreaks in Uganda, emphasizing the need for targeted interventions, strengthened surveillance, and interdisciplinary collaboration. Despite significant number of studies on RVF outbreaks and prevalence over recent years, little is known about the virus’s maintenance mechanisms in the absence of visible outbreaks. Potential reservoirs, vector dynamics, and environmental factors that facilitate its survival and re-emergence remain poorly characterized. Addressing these gaps is critical to improving early warning systems, guiding targeted surveillance, and implementing effective control measures to mitigate future outbreaks.
Population genomics uncovers loci for trait improvement in the indigenous African cereal tef (Eragrostis tef)
(Journal Article, 2025-05-26) Jones, M.R.W.; Kebede, W.; Teshome, Abel; Girija, A.; Teshome, A.; Girma, D.; Brown, J.K.M.; Quiroz-Chavez, J.; Jones, Christopher S.; Wulff, B.B.H.; Assefa, K.; Tadele, Z.; Mur, L.A.J.; Chanyalew, S.; Uauy, C.; Shorinola, Oluwaseyi
Tef (Eragrostis tef) is an indigenous African cereal that is gaining global attention as a gluten-free “superfood” with high protein, mineral, and fibre contents. However, tef yields are limited by lodging and by losses during harvest owing to its small grain size (150× lighter than wheat). Breeders must also consider a strong cultural preference for white-grained over brown-grained varieties. Tef is relatively understudied with limited “omics” resources. Here, we resequence 220 tef accessions from an Ethiopian diversity collection and also perform multi-locational phenotyping for 25 agronomic and grain traits. Grain metabolome profiling reveals differential accumulation of fatty acids and flavonoids between white and brown grains. k-mer and SNP-based genome-wide association uncover important marker-trait associations, including a significant 70 kb peak for panicle morphology containing the tef orthologue of rice qSH1—a transcription factor regulating inflorescence morphology in cereals. We also observe a previously unknown relationship between grain size, colour, and fatty acids. These traits are highly associated with retrotransposon insertions in homoeologues of TRANSPARENT TESTA 2, a known regulator of grain colour. Our study provides valuable resources for tef research and breeding, facilitating the development of improved cultivars with desirable agronomic and nutritional properties.
Whole genome resequencing of a global collection of Napier grass (Cenchrus purpureus) to explore global population structure and QTL governing yield and feed quality traits
(Journal Article, 2025) Teshome, Abel; Lire, H.; Higgins, J.; Olango, T.; Habte, Ermias H.; Negawo, Alemayehu T.; Muktar, Meki S.; Assefa, Yilikal; Pereira, J.F.; Azevedo, A.L.S.; Machado, J.C.; Nyamongo, D.; Zhang, J.; Qi, Y.; Anderson, W.; De Vega, J.; Jones, Christopher S.
Napier grass (Cenchrus purpureus) is a C4 perennial grass species native to Sub-Saharan Africa (SSA) and widely used for feed cattle in the region. In this study, we sequenced the genomes of 450 Napier grass individuals from 18 countries, identifying over 170 million DNA variants (SNPs and Indels). Approximately 1% of these SNPs were informative and used to assess genetic diversity within the collection. Our resequencing study provided valuable insights into the global genetic diversity of Napier grass. Additionally, a genome-wide association study on two independent populations identified multiple quantitative trait loci (QTL) significantly associated with key agronomic traits, including biomass yield, nitrogen and cellulose content. These findings serve as a crucial resource for preserving and understanding Napier grass genetic diversity in the context of climate change. Moreover, they will support genomics-based breeding programs aimed at developing high-yielding and drought-tolerant varieties for forage and biofuel production.
Molecular characterization of a synthetic neutralizing antibody targeting p67 of Theileria parva
(Journal Article, 2025-06) Miersch, S.; Singer, A.U.; Chen, C.; Fellouse, F.; Gopalsamy, A.; Costa, L.S. e; Lacasta, Anna; Chege, Hannah; Chege, Naomi; Nene, Vishvanath; Sidhu, S.S.
The Theileria parva sporozoite surface antigen p67 is a target of the bovine humoral immune response that generates antibodies capable of providing protection against subsequent infection. As a result, p67 has been the subject of efforts aimed at the development of an anti-sporozoite subunit vaccine. Previous studies have identified neutralizing epitopes in the N- and C-terminal regions of the full-length protein and shown that immunization with a C-terminal fragment of p67 (p67C) alone is capable of eliciting protection. To identify additional neutralizing epitopes in p67C, selections were conducted against it using a phage-displayed synthetic antibody library. An antibody that neutralized the sporozoite in vitro was identified, and the crystal structure of a Fab:peptide complex was elucidated. Mutagenesis studies aimed at validating and further characterizing the Fab:peptide interaction identified critical residues involved in binding and neutralization. This study also validates distinct epitopes for previously reported neutralizing antibodies.
Sleeping sickness in Uganda: revisiting current and historical distributions
(Journal Article, 2007-07-13) Berrang-Ford, Lea; Odiit, Martin; Maiso, Faustin; Waltner-Toews, David; McDermott, John J.
Background: Sleeping sickness is a parasitic, vector-borne disease, carried by the tsetse fly and prevalent in sub-Saharan Africa. The disease continues to pose a public health burden in Uganda, which experienced a widespread outbreak in 1900-1920, and a more recent outbreak in 1976-1989. The disease continues to spread to uninfected districts. Objectives: This paper compares the spatial distributions of sleeping in Uganda for the 1900-1920 outbreak period with current disease foci, and discusses information gaps and implications arising for future research, prevention and control. Methods: Population census records for 1911 and sleeping sickness records from Medical and Sanitary Reports of the Ugandan Protectorate for 1905-1936 were extracted from the Uganda Archives. Current sleeping sickness distribution data were provided by the Ministry of Health, Uganda. These were used to develop sleeping sickness distribution maps for comparison between the early 1900s and the early 2000s. Results: The distribution of sleeping sickness from 1905-1920 shows notable differences compared to the current distribution of disease. In particular, archival cases were recorded in south-west and central Uganda, areas currently free of disease. The disease focus has moved from lakeshore Buganda (1905-1920) to the Busoga and south-east districts. Conclusions: Archival sleeping sickness distributions indicate the potential for a much wider area of disease risk than indicated by current disease foci. This is compounded by an absence of tsetse distribution data, continued political instability in north-central Uganda, continued spread of disease into new districts, and evidence of the role of livestock movements in spreading the parasite. These results support concerns as to the potential mergence of the two disease foci in the south-east and north-west of the country.
Comparative genomics reveals common diversity and adaptation to harsh environments in the Arabian Peninsula indigenous chickens
(Journal Article, 2025-06) Assiri, A.; Vallejo-Trujillo, A.; Al-Abri, M.; Bahbahani, H.; Almathen, F.; Ahbara, A.; Al Marzooqi, W.; Tijjani, A.; Lawal, R.; Hanotte, Olivier H.
Identifying genomic regions under selection is crucial for comprehending the evolutionary history of the domestic chicken. Arabian Peninsula (AP) indigenous chickens are mostly found outdoors, being reared alongside other livestock for production purposes. These birds show high resilience to extreme temperatures (hot and cold), typical of the desert environment. The selection pressures responsible for unique local adaptations in these birds remain largely unidentified. Here, we aimed to investigate the genome diversity and structure of 15 indigenous chicken populations including 13 populations from the AP (n = 5), Ethiopia (n = 6), and the People's Republic of China (n = 2). We also included two commercial chicken populations, Fayoumi (selected for heat tolerance) and Chantecler (known for its cold tolerance). Principal component (PC) analysis separated all the populations based on their geographic areas of origin. PC1 separates the Ethiopian populations from the Chinese and AP populations, while PC2 separates the AP populations from the Chantecler, and the Ethiopian populations from the Dulong and Chantecler. The genome-wide signatures of analyses identified many candidate regions under positive selection. They include genes that may be associated with thermotolerance. These are involved in energy balance and metabolism (SUGCT, HECW1, MMADHC), cells apoptosis (APP, SRBD1, NTN1, PUF60, SLC26A8, DAP, SUGCT), angiogenesis (RYR2, LDB2, SOX5), skin protection to solar radiation (FZD10, BCO2, WNT5B, COL6A2, SIRT1) as well as growth (NELL1). Our findings suggest that Arabian chicken populations have a distinct gene pool polymorphism in relation to their adaptation to the harsh climatic environments of the AP.
Network analysis of small ruminant movements in Uganda: Implications for control of transboundary animal diseases
(Journal Article, 2025-01) Nkamwesiga, Joseph; Rascón-García, K.; Lumu, P.; Kiara, Henry K.; Perez, A.; Muhanguzi, D.; Roesel, Kristina
Domestic animals are moved for reasons that are mutually beneficial to the animal and the farmer. Some examples include the need for fresh grazing grounds and watering points, or the need to access livestock markets for income to sustain farmers’ livelihoods. However, livestock mobility is a key risk factor for the transmission of transboundary animal diseases. Contact tracing of individual animals and flocks is very challenging, especially in most low-income countries, due to a lack of efficient livestock traceability systems. Despite these challenges, low-income countries, such as Uganda, issue paper-based animal movement permits (AMPs) to ensure only clinically healthy animals are moved following a physical inspection. In this study, we used national approximately 9 years of (2012–2020) small ruminant movement data obtained from archived AMPs in Uganda to describe small ruminant movement networks. The movement networks were described using social network analysis (SNA) approaches implemented in R software to identify and visualize relationships between individual and groups districts in Uganda. Lira, Kaberamaido, Nabilatuk, Mbarara, Kiruhura, Kampala, and Wakiso were identified as districts with the highest degree (in and out-degree) and betweenness among other centrality measures. Our results suggest these districts could be the most important bridges connecting the various regions of the country. Tailoring control interventions to such districts with high incoming and high outgoing shipments, or bridges, would accelerate the nation’s ability to timely detect outbreaks, prevent or mitigate further spread, and contain diseases in their original foci, respectively. We also identified areas for active surveillance, vaccination, quarantine, and biosecurity measures-staging depending on prevailing circumstances. These findings will be used to guide the national small ruminant infectious diseases control strategies and subsequently contribute to national and global initiatives, such as the 2030 Peste des petits ruminants (PPR) eradication program.
Gene-modified genotype II live attenuated African swine fever virus induces cross-protection against genotype I but not against genotype IX
(Journal Article, 2025-12) Rathakrishnan, A.; Hemmink, Johanneke D.; Petrovan, V.; Reis, A.L.; Dixon, L.K.
African swine fever virus originated in a wildlife cycle in East Africa and spread to domestic pigs. At least twenty-three genotypes are present in Africa whereas only genotypes I and II have spread to other continents. Vaccine development has been directed mainly to genotype II. The ability of genotype II vaccines to induce cross-protection against other genotypes is unknown. Here, we compared cross-protection induced in pigs by an attenuated multiple gene-deleted genotype II modified live vaccine candidate against challenge with different genotypes. Protection against homologous virulent genotype II virus was 100%. Cross-protection against virulent genotype I virus varied between 57 and 71%. However, no protection was achieved against genotype IX challenge. The results indicate potential for use of vaccines in regions where genotypes I and II are circulating.
Engaging scientists in science policy: Experiences From Canada
(Journal Article, 2025-04-25) Lam, Steven; Raza, S.; Hansen, L.
Background: Training scientists in science policy is crucial to enhance scientific advice for decision-making. However, there are limited opportunities for scientists to receive such training. Analysis: We reflected on our participation in a one-year postgraduate science policy fellowship program in Canada. Although recently discontinued in 2023, this fellowship allowed us to refine practical policy skills, contribute to policy outputs that advanced our office’s mandate, and access career pathways beyond academia. Policy Options: Recognizing the value of engaging scientists in policy, we advocate for continued offerings of science policy training, alongside rigorous evaluation to inform program changes. Additionally, we encourage increased financial support early on for graduate students to sustain a talent pool of scientists who will become future science policy leaders. Lastly, we urge more scientists and students to be active in science policy spaces. Conclusion: By openly sharing our experiences and learnings from the fellowship, we seek to contribute to ongoing discussions on the importance of science policy training and its role in bridging the gap between science and decision-making.
Effects of livestock related gender roles on pastoral children and their implication to RVF risk exposure
(Journal Article, 2025-05-09) Mutambo, Irene N.; Bett, Bernard; Bukachi, S.A.
Background: Children in pastoral communities play a significant role in herding livestock, placing them at a high risk of exposure to zoonotic pathogens such as the Rift Valley fever (RVF) virus. However, socioeconomic studies on knowledge, attitude and practices on RVF often involve adults and community trainings that are usually implemented to bridge knowledge gaps seldom involve children. Understanding how gender roles influence risk exposure is crucial for developing effective prevention strategies. Aim: This study sought to investigate how gender roles influence the vulnerability of pastoralist boys and girls to RVF in Isiolo County, Kenya. Specifically, the study sought to examine how the livestock-related roles of boys and girls in the pastoralist communities increase their risk of RVF, establish the knowledge that pastoralist boys and girls have about RVF and assess how livestock roles affect the lives of boys and girls in the pastoral communities. Methods: A cross-sectional qualitative study was conducted in Isiolo County, Kenya. Data were collected using Focus Group Discussions (FGDs) with vignettes and key informant guides. Twelve sex-disaggregated focus group discussions of 106 discussants and 17 key informants were conducted. Data was transcribed, coded and analyzed in NVivo 14. Findings: We found that boys and girls had varying levels of knowledge about RVF, with boys showing a deeper understanding of RVF. Both girls and boys engage in livestock roles that expose them to RVF risk. Beyond RVF, pastoralism affects children’s access to education, health, and leisure time and exposes them to food insecurity. Conclusion: We conclude that both boys and girls face RVF risk, highlighting the need for targeted interventions and strategies that move beyond a general approach to RVF prevention within pastoralist communities. This is vital, as exposure pathways and vulnerabilities may differ due to gendered roles and responsibilities.
Factors associated with knowledge, attitudes, and practices of mixed crop-livestock farmers on Crimean Congo hemorrhagic fever (CCHF) and other zoonoses in Burkina Faso
(Journal Article, 2025-06) Ilboudo, Abdoul K.; Dione, Michel M.; Nijhof, A.M.; Groschup, M.H.; Traoré, O.; Ilboudo, Guy S.; Tarnagda, Z.; Savadogo, M.; Bett, Bernard K.
Background: The burden of zoonotic diseases remains high in low and middle-income countries. Among the prevalent zoonoses, Crimean-Congo hemorrhagic fever (CCHF) can pose economic and health threats, particularly among at-risk professionals. We aimed to assess the knowledge, attitudes, and practices regarding CCHF and other zoonoses among mixed-crop livestock farmers in the rural settings of Burkina Faso. Methods: A cross-sectional study that involved selected households from sixteen villages was conducted. Consenting participants aged six and above were randomly included, and a structured questionnaire that collected socio-economic data, knowledge, attitudes, and practices concerning CCHF and other zoonoses was administered. Two index outcome variables were created based on an elaborated scale: i) attitudes and practices at risk of CCHF; and ii) knowledge toward zoonoses. Descriptive statistics were performed, and univariable ordinary least squares (OLS) and seemingly unrelated regression (SUR) were used for univariable and multivariable modeling, respectively, to assess the drivers of both outcomes. Results: Of the 717 respondents, 66.4 % were male, and 20.4 % were under 15 years old. The attitudes and practices at risk were high (48.1 %), and the knowledge toward zoonoses was limited for 47.8 % of the farmers. Our multivariable SUR model shows higher odds of attitudes and practices at risk of CCHF among men (Coef [95 %CI] = 2.85[2.14;3.56]; p-value<0.001). This risk increases with the distance of the livestock grazing area, and among the households owning their livestock grazing area (Coef [95 %CI] = 1.57[0.47;2.66]; p-value = 0.005). The farmer's age (Coef[95 % CI] = 0.02[0.002;0.04]; p-value = 0.028), the male gender (Coef 95 %CI] = 1.5[0.94;2.14]; p-value<0.001), the household's farming surface (Coef[95 %CI] = 0.03[0.002;0.6]; p-value = 0.032), were the significant factors driving knowledge of zoonoses among the farmers. Conclusion: The study reveals a concerning high-risk behavior associated with CCHF among mixed-crop livestock farmers in rural Burkina Faso. The identified socio-demographic drivers underscore the importance of targeted educational and preventive measures to mitigate the impact of CCHF in this vulnerable population.
Characterization of SARS-CoV-2 intrahost genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population
(Journal Article, 2025) Lugano, Doreen; Mwangi, Kennedy; Mware, Bernard; Kibet, Gilbert; Osiany, Shebbar; Kiritu, Edward; Dobi, Paul; Muli, Collins; Njeru, Regina; Oliveira, T. de; Njenga, M.K.; Routh, A.; Oyola, Samuel O.; Schultz-Cherry, Stacey
Vaccination is a key control measure of coronavirus disease 2019 by preventing severe effects of disease outcomes, reducing hospitalization rates and death, and increasing immunity. However, vaccination can affect the evolution and adaptation of SARS-CoV-2 largely through vaccine-induced immune pressure. Here, we investigated intrahost recombination and single nucleotide variations (iSNVs) on the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome in non-vaccinated and vaccinated sequences from the Kenyan population to profile intrahost viral genetic evolution and adaptations driven by vaccine-induced immune pressure. We identified recombination hotspots in the S, N, and ORF1a/b genes and showed the genetic evolution landscape of SARS-CoV-2 by comparing within- and inter-wave recombination events from the beginning of the pandemic (June 2020 to December 2022) in Kenya. We further reveal differential expression of recombinant RNA species between vaccinated and non-vaccinated individuals and perform an in-depth analysis of iSNVs to identify and characterize the functional properties of non-synonymous mutations found in ORF-1 a/b, S, and N genes. Lastly, we detected a minority variant in non-vaccinated patients in Kenya, with an immune escape mutation S255F of the spike gene, and showed differential recombinant RNA species. Overall, this work identified unique in vivo mutations and intrahost recombination patterns in SARS-CoV-2, which could have significant implications for virus evolution, virulence, and immune escape.
Enhancing community awareness of antimicrobial use and resistance through community conversations in rural Ethiopia
(Journal Article, 2025-05-06) Lemma, Mamusha; Alemu, Biruk; Amenu, Kebede; Wieland, Barbara; Knight-Jones, Theodore J.D.
Background: Enhanced availability of veterinary drugs in Ethiopia has led to a growing use of these drugs in food-producing animals. However, the use of drugs in livestock is not commonly supervised by trained veterinarians. In addition, smallholder livestock producers often lack sufficient education and information about antimicrobial use to achieve the intended impact. Methods: We used Community Conversations to raise awareness and knowledge about antimicrobial use and resistance within rural communities. We used single-sex and mixed-gender discussion groups to explore community members’ perceptions and practices regarding antimicrobial use and resistance. Results: The data revealed knowledge and behavioral patterns in antimicrobial use and resistance, which vary between communities based on gender roles and information sources. Initially, antimicrobial resistance was poorly understood, but gradually, frequent drug use, poor-quality medications, poor regulatory system, and poor veterinary service emerged as key contributors. Although communities recognized the importance of preventive measures to reduce antimicrobial use, knowledge gaps and resource constraints limit their implementation. Conclusions: Raising awareness and knowledge within rural communities is an effective approach to promoting behavior change about antimicrobial use and resistance. The insights gained from understanding community perceptions and practices can help develop targeted education and training programs for stakeholders involved in the antimicrobial supply chain.
How good are livestock statistics in Africa? Can nudging and direct counting improve the quality of livestock asset data?
(Journal Article, 2025-05) Abay, Kibrom A.; Ayalew, Hailemariam; Terfa, Zelalem; Karguia, Joseph; Breisinger, Clemens
Livestock statistics in most low- and middle-income countries rely on self-reported, survey-based measures. However, respondents may have various challenges to accurately report livestock ownership. This study introduces a novel set of survey and measurement experiments to improve livestock statistics in Africa. We introduce two innovations to conventional livestock data collection methods. First, we address some of the sources of potential underreporting in livestock assets by introducing an explicit nudge to a random subset of survey respondents. Second, we arrange for direct counting of livestock assets by enumerators and local livestock experts. We demonstrate that self-reported data on livestock ownership suffer from significant and systematic underreporting. While our nudge affects only the reporting behaviour of households with larger stocks of livestock, direct counting increases total livestock ownership by 39 percent and the reported number of cattle by 43 percent. These impacts are evident at both the extensive and intensive margins of livestock asset ownership, as well as considering the number and value of livestock assets owned. Such mismeasurement in self-reported livestock data can lead to underestimation of the contribution of the livestock sector to national economies. Furthermore, direct counting generates important spillover effects to livestock species not explicitly counted in the survey. We finally show that underreporting in self-reported livestock data is systematic and hence consequential for statistical inferences. Our findings underscore that survey designs that can address specific sources of bias in self-reported livestock data can meaningfully improve livestock asset measurement in Africa.
Lamb survival and ewe longevity in a crossbreeding program between indigenous and exotic sheep in semi-arid lands
(Journal Article, 2025-08) Oyieng, Edwin P.; Ojango, Julie M.K.; Gauly, M.; Mrode, Raphael A.; Okeyo Mwai, Ally; König, S.
The survival of lambs and longevity of ewes within flocks are important for the sustainability of sheep populations especially in arid and semi-arid lands (ASAL). In this study we conducted pre- and post-weaning survival analysis of lambs and the longevity of ewes of indigenous pure Red Maasai (RRRR), pure Dorper (DDDD), and their crosses comprising F1 (DDRR) and 75%Dorper-25%Red Maasai (DDDR) using Cox and Weibull proportional hazard models. The objective was to determine the genetic and non-genetic factors affecting lamb survival to yearling as well as ewe longevity. Data comprised records on 6,313 lambs and 2,003 ewes. Overall pre-weaning mortality was lower (5%) compared to post-weaning mortality rate (17%). Lambs born during the long dry season had a higher risk of dying than those born during the wet seasons. For both lambs and ewes, the Dorper had the highest risk of dying or being culled. Among the crossbreds, the DDDR lambs and ewes had higher risks of dying or being culled relative to F1 lambs and ewes. The risk of ewes being culled reduced with increasing age at first lambing and parity. Heritability estimates for pre-weaning mortality were higher (0.10 - 0.14) than post-weaning mortality (0.01 - 0.05). The higher heritability for pre-weaning lamb survival in indicates greater genetic variation, presenting an opportunity for selection for lamb survival. Interventions to improve the production environment in the ASAL areas would also improve the survival of lambs and longevity of ewes.
Growth curve fitting and analysis of intestinal flora changes of the Magang Goose (Anser domesticus) during 1 to 70 days post hatch
(Journal Article, 2025-08) Li, X.; Song, G.; Cao, Q.; Mo, Q.; Fu, Y.; Chen, J.; Lukuyu, Ben A.; Wang, S.; Ye, H.; Zhu, Y.; Muhammad, K.S.; Yang, L.; Pan, J.; Wang, W.
Nonlinear models are frequently utilized to study the growth and development of livestock and poultry, and to investigate the dynamic relationship with the intestinal microbiota changes. In this study, a total of 180 Magang geese (1-day-old) were selected and randomly divided into 6 replicates with 30 geese in each replicate. The growth performance, organ development, and intestinal flora composition of geese aged 7, 14, 21, 28, 42, 50, 60, and 70 d were observed. A total of 3 nonlinear growth models were applied to fit the development curves, aiming to explore the ontogenic development of Magang geese and the dynamic changes in the intestinal flora. Our results demonstrated that the Gompertz model serves as the most suitable model for simulating the growth pattern of Magang geese (R²=0.996). Using this model, the weight of the inflection point in Magang geese was 3.470 kg, the age of the inflection point was 25.460d, and the maximum daily gain was 0.061 kg. The development curves of the liver, kidney, and pancreas conform to the Logistic model (R²=0.901, 0.978, 0.971), while the intestinal development also followed this model. The bacteria involved in energy metabolism (Subdoligranulum, Bacteroides, Romboutsia) and the bacteria inhibiting the colonization of harmful bacteria (Blautia) in cecum changed rapidly from 7 to 14 d, and microbial community composition stabilized after 21 d. In conclusion, our findings indicated that the ontogenic pattern of the Magang goose conformed to the Gompertz growth curve. The period from 7 to 42 d represents the rapid growth phase for Magang geese, during which organ development occurs, and cecal microbiota composition becomes increasingly stable.
Seroprevalence and risk factor modeling of Marek’s disease virus in indigenous Tilili breed chickens of the Amhara Region, Ethiopia
(Journal Article, 2025-06) Berrie, K.; Jemberu, Wudu T.; Shite, A.; Admassu, B.; Melaku, A.; Birhan, M.; Getenet, K.; Fenta, M.D.; Kinde, M.Z.; Bitew, A.B.; Mulaw, A.; Mekasha, Y.T.
This study aims to assess the seroprevalence and potential risk factors associated with Marek’s disease occurrence in indigenous Tilili breed chickens and its crosses. A cross-sectional serological study and questionnaire survey were conducted in seven districts of the Amhara region, Ethiopia, from November 2023 to June 2024. Using multi-stage sampling, 17 Kebeles (peasant associations) were selected from the seven districts. A total of 768 chicken sera were sampled and tested for presence of Marek’s disease virus antibodies using an indirect enzyme-linked immunosorbant assay test. According to the study, the overall apparent seroprevalence of MDV was 74.6%, with Ankesha district having the lowest prevalence (57.5%) and Banja district having the highest (93.8%).The prevalence varied significantly across the studied districts, and there was a statistically significant variation in disease distribution among the peasant associations. Key risk factors associated with Marek’s disease virus seropositivity in Tilili breeds included contact with other birds in the vicinity, sex, age group, and sanitation of the housing. However, factors such as breed, rearing method, and farming type were not significantly associated with Marek’s disease sero-status. This high seroprevalence of the disease in this chicken ecotype indicates active circulation of the virus in the area, underscoring the need for stringent control measures. Further molecular studies and identification of MDV DNA in active outbreaks is critical to characterize the circulating virus and assess the economic impact of the disease on these valuable indigenous chickens of Ethiopia.
Detection of canine distemper virus (CDV) neutralising antibodies in small ruminants during peste-des-petits-ruminants virus (PPRV) surveillance in Zambia
(Journal Article, 2025-04-30) Lysholm, Sara; Logan, N.; Lindahl, Johanna F.; Berg, M.; Johansson, E.; Bergkvist, P.K.; Dautu, G.; Chazya, R.; Willett, B.J.; Munyeme, M.; Wensman, J.J.
Canine distemper virus (CDV) is endemic in Zambia, while peste-des-petits-ruminants virus (PPRV) has not been detected. This study screened 962 farmed goats and 237 small ruminants at informal markets for PPRV antibodies using c-ELISA. A subset (n = 29) was re-analysed with virus neutralisation assays (VNA) for antibodies to PPRV and CDV due to cross-reactivity concerns. c-ELISA indicated 6.44% PPRV seroprevalence on farms and 3.80% at markets. While VNA detected no PPRV antibodies, 45% (13/29) tested positive for CDV, possibly suggesting cross-reactivity. Given the study’s limitations, further research is needed to determine whether PPRV is present in Zambia and assess potential cross-reactivity.

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