Epidemiology of Bovine viral Diarrhoea in Tanzania small holder dairy sector

牛病毒性腹泻是由黄病毒科瘟病毒属的牛病毒性腹泻病毒（BVDV）引起的，是世界范围内最重要的牛疾病之一，可导致成年牛繁殖性能差和小牛粘膜疾病。此外，它还导致免疫抑制和对其他感染的易感性增加，其影响尚不确定，特别是在撒哈拉以南非洲，与欧洲相比，那里的动物暴露于更广泛和更高强度的感染。之前没有对坦桑尼亚牛中BVDV血清阳性率的估计。我们目前正在坦桑尼亚7个集群的小型保持器奶牛群体中收集样本，作为CTLGH和ADGG项目下BMGF/DFID资助项目的一部分。在阿鲁沙地区（我们研究的第一个地区），流产和早期小牛死亡率约为6.7%（95% CI 4.1-10.7），其中三分之一是活产小牛，存活不超过一个月。关于SSA中BVD的已发表数据很少，但之前在喀麦隆进行的一项研究发现，基于“斑点"检测方法，在过去一年中，牛血清水平和牛群内血清阳性率分别为92%和30%，16.5%的牛群被归类为牛群中有持续感染的小牛（PI）[1]。在肯尼亚小型保持器牛中进行的另一项研究发现，1岁小牛的血清阳性率约为20（已存活至该年龄），并且BVD与小牛呼吸道综合征中的其他呼吸道病毒密切相关[2]小型保持器奶牛场系统是坦桑尼亚相对较新的农业系统，是从高性能品种（如弗里斯兰和艾尔夏）的牛分配方案中发展出来的，与当地品种随机杂交，对它们对BVD的易感性或其在该系统中可能产生的影响知之甚少。拟议的项目将筛选储存在ILRI和NM-AIST的库存血清和血液样本中的BVD病毒抗体和病毒序列。使用年龄，位置，产犊历史等相关的个体动物数据，他们将开发统计和动态模型，以确定风险因素，并估计该系统中疾病的传播参数和经济影响。此外，每个动物的Illumina 50 K SNP数据允许在该人群中进行一些基本的遗传关联研究[3]。该项目将为学生提供一系列培训经验，包括湿实验室诊断，流行病学和建模以及遗传分析。也有可能进行一项小型试点研究，在目前的研究环境中从有限地理区域的小牛中收集样本，并使用宏基因组学方法更好地了解早期死亡情况下存在的病原体。[1]Handel et al.（2011）喀麦隆Adamawa地区牛病毒性腹泻病毒（BVDV）的血清流行病学和SPOT试验用于鉴定PI小牛的牛群。PLoS ONE 6（7）：e21620. doi：10.1371/journal.pone.0021620[2] R. Callaby et al.（2016）Research in Veterinary Science 108：120-124[3] Murray et al.（2013）Genetic susceptibility to infectious disease in East African Shorthorn Zebu：a genome-wide analysis of the effect of heterozygosity and exotic introgression. BMC进化生物学13：246.

Bovine viral diarrhoea, caused by the bovine viral diarrhoea virus (BVDV) in the Pestivirus genus of the Flaviviridae, is one of the most important diseases of cattle worldwide causing poor reproductive performance in adult cattle and mucosal disease in calves. In addition, it causes immunosuppression and increased susceptibility to other infections, the impact of which is uncertain, particularly in sub-Saharan Africa where animals are exposed to a much wider range and higher intensity of infections compared to Europe. There are no previous estimates of the seroprevalence of BVDV in cattle in Tanzania.We are currently collecting samples from small holder dairy cattle populations in 7 clusters across Tanzania as part of a BMGF/DFID funded project under the CTLGH and ADGG programmes. Abortion and early calf mortality rates are ~ 6.7% (95% CI 4.1-10.7) in Arusha Region (the first we have examined) and a third of these are live calf births that do not survive more than a month. There is little published data on BVD in SSA but a previous study in Cameroon found herd-level and within herd seroprevalences of 92% and 30% respectively and 16.5% of herds were classed as having a persistently infected calf (PI) in the herd within the last year based on the ''spot'' test approach [1]. Another study in Kenyan small holder cattle found seroprevalence of ~20% in year old calves (that had survived to this age) and that BVD was strongly associated with other respiratory viruses in the calf respiratory syndrome [2].The small holder dairy system is a relatively new farming system in Tanzania and has developed out of programmes of cattle distribution of high performing breeds such as Friesian and Ayrshire that have been crossed in a haphazard way with local breeds and little is know of their susceptibility to BVD or the impact it may have in this system.The proposed project would screen the banked sera and blood samples stored at ILRI and NM-AIST for antibodies to BVD virus and viral sequences. Using the associated individual animal data on age, location, calving history etc they would develop statistical and dynamic models to identify risk factors and estimate transmission parameters and economic impact of the disease in this system. In addition there is Illumina 50K SNP data for each animal allowing some basic genetic association studies in this population [3].This project would provide the student with a range of training experience include wet lab diagnostics, epidemiology and modelling and genetic analysis. There would also be the potential for a small pilot study to collect samples from calves in a limited geographical area in the current study setting and use metagenomics approaches to better understand pathogens present in early mortality situations.[1] Handel et al. (2011) Seroepidemiology of Bovine Viral Diarrhoea Virus (BVDV) in the Adamawa Region of Cameroon and Use of the SPOT Test to Identify Herds with PI Calves. PLoS ONE 6(7): e21620. doi:10.1371/journal.pone.0021620[2] R. Callaby et al. (2016) Research in Veterinary Science 108: 120-124[3] Murray et al. (2013) Genetic susceptibility to infectious disease in East African Shorthorn Zebu: a genome-wide analysis of the effect of heterozygosity and exotic introgression. BMC Evolutionary Biology 13:246.