人类杯状病毒分型工具：一种基于网络的用于基因分型人类诺如病毒和沙波病毒序列的工具。
Human Calicivirus Typing tool: A web-based tool for genotyping human norovirus and sapovirus sequences.
机构信息
Cherokee Nation Assurance, Arlington, VA, 22202, USA; Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
出版信息
J Clin Virol. 2021 Jan;134:104718. doi: 10.1016/j.jcv.2020.104718. Epub 2020 Dec 13.
BACKGROUND
The family Caliciviridae consists of a genetically diverse group of RNA viruses that infect a wide range of host species including noroviruses and sapoviruses which cause acute gastroenteritis in humans. Typing of these viruses relies on sequence-based approaches, and therefore there is a need for rapid and accurate web-based typing tools.
OBJECTIVE
To develop and evaluate a web-based tool for rapid and accurate genotyping of noroviruses and sapoviruses.
METHODS
The Human Calicivirus Typing (HuCaT) tool uses a set of curated reference sequences that are compared to query sequences using a k-mer (DNA substring) based algorithm. Outputs include alignments and phylogenetic trees of the 12 top matching reference sequences for each query.
RESULTS
The HuCaT tool was validated with a set of 1310 norovirus and 239 sapovirus sequences covering all known human norovirus and sapovirus genotypes. HuCaT tool assigned genotypes to all queries with 100 % accuracy and was much faster (17 s) than BLAST (150 s) or phylogenetic analyses approaches.
CONCLUSIONS
The web-based HuCaT tool supports rapid and accurate genotyping of human noroviruses and sapoviruses.
背景
小核糖核酸病毒科由一组遗传上多样化的 RNA 病毒组成，这些病毒感染包括诺如病毒和肠型杯状病毒在内的广泛宿主物种，这些病毒会导致人类急性肠胃炎。这些病毒的分型依赖于基于序列的方法，因此需要快速准确的基于网络的分型工具。
目的
开发和评估一种用于快速准确分型诺如病毒和肠型杯状病毒的基于网络的工具。
方法
人类杯状病毒分型（HuCaT）工具使用了一组经过精心整理的参考序列，这些序列与查询序列使用基于 k-mer（DNA 子字符串）的算法进行比较。输出包括每个查询的 12 个最佳匹配参考序列的比对和系统发育树。
结果
HuCaT 工具用涵盖所有已知人类诺如病毒和肠型杯状病毒基因型的 1310 个诺如病毒和 239 个肠型杯状病毒序列进行了验证。HuCaT 工具对所有查询的基因型分配准确率达到 100%，比 BLAST（150 秒）或系统发育分析方法快得多（17 秒）。
结论
基于网络的 HuCaT 工具支持快速准确的人类诺如病毒和肠型杯状病毒的分型。
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