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Risk factors for rotavirus infection in pigs in Busia and Teso subcounties, Western Kenya

机译：肯尼亚西部Busia和Teso Subcounties猪轮状病毒感染的危险因素

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We analysed data that were previously collected for molecular characterisation of rotavirus (RV) groups A and C in pigs from Teso and Busia subcounties in Kenya to determine risk factors for its infection. The data included records from 239 randomly selected piglets aged between 1 and 6 months raised in free range and backyard production systems. RV infection was confirmed by screening of fresh faecal samples by using reverse transcription polymerase chain reaction (RT-PCR); selected positive samples were subsequently sequenced and used for phylogenetic analysis. In this analysis, RV infection status was used as outcome variable, while the metadata collected at the time of sampling were used as predictors. A Bayesian hierarchical model which used integrated nested Laplace approximation (INLA) method was then fitted to the data. The model accounted for the spatial effect by using stochastic partial differential equations (SPDEs). Of the 239 samples screened, 206 were available for the analysis. Descriptive analyses showed that 27.7 % (57/206) of the samples were positive for rotaviruses groups A and C, 18.5 % were positive for group A rotaviruses, 5.3 % were positive for group C rotaviruses, while 3.9 % had co-infections from both groups of rotaviruses. The spatial effect was insignificant, and a simple (non-spatial) model showed that piglets (= 4 months) and those pigs kept in free range systems had higher risk of exposure to rotavirus infection as compared to older pigs (> 4 months) and those tethered or housed, respectively. Intervention measures that will target these high-risk groups of pigs will be beneficial to farmers.
机译：我们分析了之前收集的肯尼亚特索和布西亚亚县猪轮状病毒（RV）A组和C组分子特征的数据，以确定其感染的风险因素。这些数据包括239头随机挑选的仔猪的记录，这些仔猪年龄在1到6个月之间，在自由放养和后院生产系统中饲养。通过使用逆转录聚合酶链反应（RT-PCR）筛查新鲜粪便样本，确认RV感染；随后对选定的阳性样本进行测序，并用于系统发育分析。在该分析中，RV感染状态被用作结果变量，而采样时收集的元数据被用作预测因子。然后，采用集成嵌套拉普拉斯近似（INLA）方法对数据进行贝叶斯层次模型拟合。该模型采用随机偏微分方程（SPDE）来考虑空间效应。在筛选的239个样本中，有206个可用于分析。描述性分析显示，27.7%（57/206）的样本对A组和C组轮状病毒呈阳性，18.5%对A组轮状病毒呈阳性，5.3%对C组轮状病毒呈阳性，而3.9%的样本同时感染了两组轮状病毒。空间效应不显著，一个简单的（非空间）模型显示，与年龄较大的猪（>4个月）和栓系或圈养的猪相比，小猪（

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