Influenza D virus has been identified in America, Europe, and Asia. We detected influenza D virus antibodies in cattle and small ruminants from North (Morocco) and West (Togo and Benin) Africa. Dromedary camels in Kenya harbored influenza C or D virus antibodies, indicating a potential new host for these viruses.

Inadequate facilities and hygiene at slaughterhouses can result in contamination of meat and occupational hazards to workers. The objectives of this study were to assess current conditions in slaughterhouses in western Kenya and the knowledge, and practices of the slaughterhouse workers toward hygiene and sanitation. Between February and October 2012 all consenting slaughterhouses in the study area were recruited. A standardised questionnaire relating to facilities and practices in the slaughterhouse was administered to the foreperson at each site. A second questionnaire was used to capture individual slaughterhouse workers’ knowledge, practices and recent health events. A total of 738 slaughterhouse workers from 142 slaughterhouses completed questionnaires. Many slaughterhouses had poor infrastructure, 65% (95% CI 63–67%) had a roof, cement floor and walls, 60% (95% CI 57–62%) had a toilet and 20% (95% CI 18–22%) had hand-washing facilities. The meat inspector visited 90% (95% CI 92–95%) of slaughterhouses but antemortem inspection was practiced at only 7% (95% CI 6–8%). Nine percent (95% CI 7–10%) of slaughterhouses slaughtered sick animals. Only half of workers wore personal protective clothing - 53% (95% CI 51–55%) wore protective coats and 49% (95% CI 46–51%) wore rubber boots. Knowledge of zoonotic disease was low with only 31% (95% CI 29–33%) of workers aware that disease could be transmitted from animals. The current working conditions in slaughterhouses in western Kenya are not in line with the recommendations of the Meat Control Act of Kenya. Current facilities and practices may increase occupational exposure to disease or injury and contaminated meat may enter the consumer market. The findings of this study could enable the development of appropriate interventions to minimise public health risks. Initially, improvements need to be made to facilities and practices to improve worker safety and reduce the risk of food contamination. Simultaneously, training programmes should target workers and inspectors to improve awareness of the risks. In addition, education of health care workers should highlight the increased risks of injury and disease in slaughterhouse workers. Finally, enhanced surveillance, targeting slaughterhouse workers could be used to detect disease outbreaks. This “One Health” approach to disease surveillance is likely to benefit workers, producers and consumers.

Despite only 8% of cattle being found in Europe, European breeds dominate current genetic resources. This adversely impacts cattle research in other important global cattle breeds, especially those from Africa for which genomic resources are particularly limited, despite their disproportionate importance to the continent’s economies. To mitigate this issue, we have generated assemblies of African breeds, which have been integrated with genomic data for 294 diverse cattle into a graph genome that incorporates global cattle diversity. We illustrate how this more representative reference assembly contains an extra 116.1 Mb (4.2%) of sequence absent from the current Hereford sequence and consequently inaccessible to current studies. We further demonstrate how using this graph genome increases read mapping rates, reduces allelic biases and improves the agreement of structural variant calling with independent optical mapping data. Consequently, we present an improved, more representative, reference assembly that will improve global cattle research.

Background: In many parts of the developing world, pigs are kept under low-input systems where they roam freely to scavenge food. These systems allow poor farmers the opportunity to enter into livestock keeping without large capital investments. This, combined with a growing demand for pork, especially in urban areas, has led to an increase in the number of small-holder farmers keeping free range pigs as a commercial enterprise. Despite the benefits which pig production can bring to a household, keeping pigs under a free range system increases the risk of the pig acquiring diseases, either production-limiting or zoonotic in nature. This study used Global Positioning System (GPS) technology to track free range domestic pigs in rural western Kenya, in order to understand their movement patterns and interactions with elements of the peri-domestic environment. Results: We found that these pigs travel an average of 4,340 m in a 12 hr period and had a mean home range of 10,343 m² (range 2,937–32,759 m²) within which the core utilisation distribution was found to be 964 m² (range 246–3,289 m²) with pigs spending on average 47% of their time outside their homestead of origin. Conclusion: These are the first data available on the home range of domestic pigs kept under a free range system: the data show that pigs in these systems spend much of their time scavenging outside their homesteads, suggesting that these pigs may be exposed to infectious agents over a wide area. Control policies for diseases such as Taenia solium, Trypanosomiasis, Trichinellosis, Toxoplasmosis or African Swine Fever therefore require a community-wide focus and pig farmers require education on the inherent risks of keeping pigs under a free range system. The work presented here will enable future research to incorporate movement data into studies of disease transmission, for example for the understanding of transmission of African Swine Fever between individuals, or in relation to the life-cycle of parasites including Taenia solium.

More people globally depend on the water buffalo than any other domesticated species, and as the most closely related domesticated species to cattle they can provide important insights into the shared evolutionary basis of domestication. Here, we sequence the genomes of 79 water buffalo across seven breeds and compare patterns of between breed selective sweeps with those seen for 294 cattle genomes representing 13 global breeds. The genomic regions under selection between cattle breeds significantly overlap regions linked to stature in human genetic studies, with a disproportionate number of these loci also shown to be under selection between water buffalo breeds. Investigation of potential functional variants in the water buffalo genome identifies a rare example of convergent domestication down to the same mutation having independently occurred and been selected for across domesticated species. Cross-species comparisons of recent selective sweeps can consequently help identify and refine important loci linked to domestication.

Evidence suggests that the intracellular bacterial pathogen Coxiella burnetii (which causes Q fever) is widespread, with a near global distribution. While there has been increasing attention to Q fever epidemiology in high-income settings, a recent systematic review highlighted significant gaps in our understanding of the prevalence, spatial distribution and risk factors for Q fever infection across Africa. This research aimed to provide a One Health assessment of Q fever epidemiology in parts of Western and Nyanza Provinces, Western Kenya, in cattle and humans. A cross-sectional survey was conducted: serum samples from 2049 humans and 955 cattle in 416 homesteads were analysed for C. burnetii antibodies. Questionnaires covering demographic, socio-economic and husbandry information were also administered. These data were linked to environmental datasets based on geographical locations (e.g., land cover). Correlation and spatial-cross correlation analyses were applied to assess the potential link between cattle and human seroprevalence. Multilevel regression analysis was used to assess the relationships between a range of socio-economic, demographic and environmental factors and sero-positivity in both humans and animals. The overall sero-prevalence of C. burnetii was 2.5% in humans and 10.5% in cattle, but we found no evidence of correlation between cattle and human seroprevalence either within households, or when incorporating spatial proximity to other households in the survey. Multilevel modelling indicated the importance of several factors for exposure to the organism. Cattle obtained from market (as opposed to those bred in their homestead) and those residing in areas with lower precipitation levels had the highest sero-prevalence. For humans, the youngest age group had the highest odds of seropositivity, variations were observed between ethnic groups, and frequent livestock contact (specifically grazing and dealing with abortion material) was also a risk factor. These results illustrate endemicity of C. burnetii in western Kenya, although prevalence is relatively low. The analysis indicates that while environmental factors may play a role in cattle exposure patterns, human exposure patterns are likely to be driven more strongly by livestock contacts. The implication of livestock markets in cattle exposure risks suggests these may be a suitable target for interventions. The bacteria Coxiella burnetii has a widespread distribution and causes illness in both humans and livestock (Q Fever), including long-term effects in a proportion of cases. Despite a recent resurgence in interest in a European context, there is a significant lack of understanding of the prevalence of exposure, burden of disease, or epidemiological risk factors in low-income settings. Our study provides much needed new evidence, reporting seroprevalence in a linked human and cattle population in western Kenya and identifying factors associated with increased seroprevalence in humans and cattle within this setting. Our results indicate that environmental factors may play a role in patterns of exposure in cattle populations in western Kenya, where cattle in areas with less rainfall were more likely to have evidence of previous exposure to the bacteria. However, human exposure is more likely to be influenced by livestock contact patterns. In addition, cattle brought onto a homestead following purchase at a market or another homestead had higher seroprevalence than those bred on the homestead. Further research on the role of livestock markets in disease spread is required and may form the basis for the future development of Q Fever control measures.