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Precise genotyping and recombination detection of Enterovirus

机译：肠道病毒的精确基因分型和重组检测

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Enteroviruses (EV) with different genotypes cause diverse infectious diseases in humans and mammals. A correct EV typing result is crucial for effective medical treatment and disease control; however, the emergence of novel viral strains has impaired the performance of available diagnostic tools. Here, we present a web-based tool, named EVIDENCE (EnteroVirus In DEep conception, http://symbiont.iis.sinica.edu.tw/evidence ), for EV genotyping and recombination detection. We introduce the idea of using mixed-ranking scores to evaluate the fitness of prototypes based on relatedness and on the genome regions of interest. Using phylogenetic methods, the most possible genotype is determined based on the closest neighbor among the selected references. To detect possible recombination events, EVIDENCE calculates the sequence distance and phylogenetic relationship among sequences of all sliding windows scanning over the whole genome. Detected recombination events are plotted in an interactive figure for viewing of fine details. In addition, all EV sequences available in GenBank were collected and revised using the latest classification and nomenclature of EV in EVIDENCE. These sequences are built into the database and are retrieved in an indexed catalog, or can be searched for by keywords or by sequence similarity. EVIDENCE is the first web-based tool containing pipelines for genotyping and recombination detection, with updated, built-in, and complete reference sequences to improve sensitivity and specificity. The use of EVIDENCE can accelerate genotype identification, aiding clinical diagnosis and enhancing our understanding of EV evolution.
机译：不同基因型的肠病毒（EV）在人类和哺乳动物中引起多种传染病。正确的EV分型结果对于有效的医疗和疾病控制至关重要。但是，新型病毒株的出现削弱了可用诊断工具的性能。在这里，我们介绍了一个基于Web的工具EVIDENCE（EnteroVirus In DEep的概念，http：//symbiont.iis.sinica.edu.tw/evidence），用于EV基因分型和重组检测。我们介绍了使用混合排名分数基于相关性和感兴趣的基因组区域评估原型适用性的想法。使用系统发育方法，最可能的基因型是根据所选参考文献中最接近的邻居确定的。为了检测可能的重组事件，EVIDENCE计算在整个基因组上扫描的所有滑动窗口的序列之间的序列距离和系统发育关系。将检测到的重组事件绘制在交互式图中，以查看详细信息。此外，使用EVIDENCE中最新的EV分类和命名法，收集并修订了GenBank中所有可用的EV序列。这些序列内置于数据库中，并在索引目录中进行检索，或者可以通过关键字或序列相似性进行搜索。 EVIDENCE是第一个基于Web的工具，包含用于基因分型和重组检测的流水线，并带有更新的，内置的和完整的参考序列，以提高灵敏度和特异性。 EVIDENCE的使用可以加速基因型鉴定，帮助临床诊断并增强我们对EV进化的理解。

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