Epidemiology of Bovine viral Diarrhoea in Tanzania small holder dairy sector

牛病毒性腹泻是由黄病毒科黄病毒属中的牛病毒性腹泻病毒(BVDV)引起的，是世界范围内引起成年牛繁殖性能低下和犊牛黏膜疾病的最重要的牛疾病之一。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，那里的动物暴露在更大范围和更高强度的感染中。我们目前正在从坦桑尼亚各地7个集群的小奶牛种群中收集样本，这是BMGF/DFID资助的CTLGH和ADGG方案下项目的一部分。阿鲁沙地区的流产和早期牛犊死亡率约为6.7%(95%可信区间4.1-10.7)(这是我们第一次检查)，其中三分之一是存活不到一个月的活产牛犊。关于SSA中BVD的公开数据很少，但喀麦隆之前的一项研究发现，在牛群水平和牛群内的血清流行率分别为92%和30%，16.5%的牛群在过去一年内被归类为在牛群中持续感染小牛(PI)[1]。另一项对肯尼亚小牛的研究发现，在一岁的小牛(活到这个年龄)中，血清阳性率约为20%，BVD与小牛呼吸综合征中的其他呼吸道病毒密切相关[2]。小牛饲养系统在坦桑尼亚是一个相对较新的养殖系统，它是从高性能品种的牛分配方案中发展出来的，如Friesian和Ayrshire，这些品种以随意的方式与当地品种杂交，人们对它们对BVD的易感性或它可能对该系统产生的影响知之甚少。拟议的项目将对ILRI和NM-AIST储存的BVD病毒抗体和病毒序列进行筛查。他们将利用年龄、地点、产牛史等相关的个体动物数据，开发统计和动态模型，以识别风险因素，并估计疾病在该系统中的传播参数和经济影响。此外，还有每种动物的Illumina 50K SNP数据，以便在该种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。还有可能进行一项小规模的先导性研究，在当前的研究环境中从有限的地理区域收集小牛样本，并使用元基因组学方法更好地了解早期死亡情况下存在的病原体。(2011)喀麦隆阿达马瓦地区牛病毒性腹泻病毒(BVDV)的血清流行病学，并使用现场检测来识别有小牛感染的牛群。PLOS One 6(7)：E21620。DOI：10.1371/Joural.pone.0021620[2]R.Callaby等人。(2016)兽医科学研究108：120-124[3]默里等人。(2013)东非短刺泽布对传染病的遗传易感性：杂合性和外来导入效应的全基因组分析。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.