Reconstruction of the Transmission History of RNA Virus Outbreaks Using Full Genome Sequences: Foot-and-Mouth Disease Virus in Bulgaria in 2011

Improvements to sequencing protocols and the development of computational phylogenetics have opened up opportunities to study the rapid evolution of RNA viruses in real time. In practical terms, these results can be combined with field data in order to reconstruct spatiotemporal scenarios that describe the origin and transmission pathways of viruses during an epidemic. In the case of notifiable diseases, such as foot-and-mouth disease (FMD), these analyses provide important insights into the epidemiology of field outbreaks that can support disease control programmes. This study reconstructs the origin and transmission history of the FMD outbreaks which occurred during 2011 in Burgas Province, Bulgaria, a country that had been previously FMD-free-without-vaccination since 1996. Nineteen full genome sequences (FGS) of FMD virus (FMDV) were generated and analysed, including eight representative viruses from all of the virus-positive outbreaks of the disease in the country and 11 closely-related contemporary viruses from countries in the region where FMD is endemic (Turkey and Israel). All Bulgarian sequences shared a single putative common ancestor which was closely related to the index case identified in wild boar. The closest relative from outside of Bulgaria was a FMDV collected during 2010 in Bursa (Anatolia, Turkey). Within Bulgaria, two discrete genetic clusters were detected that corresponded to two episodes of outbreaks that occurred during January and March-April 2011. The number of nucleotide substitutions that were present between, and within, these separate clusters provided evidence that undetected FMDV infection had occurred. These conclusions are supported by laboratory data that subsequently identified three additional FMDV-infected livestock premises by serosurveillance, as well as a number of antibody positive wild boar on both sides of the border with Turkish Thrace. This study highlights how FGS analysis can be used as an effective on-the-spot tool to support and help direct epidemiological investigations of field outbreaks.

测序技术流程的优化与计算系统发育学的发展，为实时研究RNA病毒的快速演化提供了新的契机。具体而言，可将此类研究结果与现场流行病学数据相结合，重构流行病暴发期间病毒的起源与传播路径相关的时空传播场景。对于口蹄疫（foot-and-mouth disease, FMD）这类法定报告传染病而言，此类分析可为田间暴发疫情的流行病学研究提供重要见解，从而助力疾病防控计划的实施。本研究针对保加利亚布尔加斯州2011年暴发的口蹄疫疫情展开溯源与传播史重构——保加利亚自1996年起便维持无口蹄疫（无疫苗免疫）状态。本研究共获取并分析了19株口蹄疫病毒（foot-and-mouth disease virus, FMDV）的全基因组序列（full genome sequences, FGS）：其中8株为保加利亚境内所有口蹄疫阳性暴发疫情的代表性毒株，另外11株为该疫情暴发同期、来自口蹄疫流行区域（土耳其与以色列）的高度同源毒株。所有保加利亚毒株共享一个推定共同祖先，且该祖先与野猪中检出的首例病例高度同源。保加利亚境外最接近的毒株为2010年在土耳其布尔萨（安纳托利亚地区）采集的口蹄疫病毒株。在保加利亚境内，研究检出两个独立的遗传簇，分别对应2011年1月以及3-4月暴发的两波疫情。这些独立遗传簇之间以及簇内的核苷酸替换数量，证明曾存在未被检出的口蹄疫病毒感染事件。上述结论得到后续实验室数据的支持：通过血清学监测，研究人员又检出3处额外的口蹄疫病毒感染牲畜养殖场，同时在与土耳其色雷斯地区接壤的边境两侧，均发现了口蹄疫抗体阳性的野猪种群。本研究凸显了全基因组序列分析可作为高效的现场工具，用于支持并指导田间暴发疫情的流行病学调查。