Genetic polymorphism across regions of the three open reading frames of "Norwalk-like viruses"
Genetic polymorphism across regions of the three open reading frames of "Norwalk-like viruses"
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DOI：
10.1007/s007050050020
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发表时间：
2000-01-01
影响因子：
2.7
通讯作者：
Koopmans, MPG
中科院分区：
文献类型：
--
作者：
Vinjé, J;Green, J;Koopmans, MPG
起源于急性胃肠炎暴发和散发性病例的诺瓦克样人类杯状病毒(NLV)的基因组特征显示出惊人的高度多样性，甚至在RNA聚合酶基因中也是如此，该基因被认为是高度保守的。由于关于抗原关系的信息有限，由于缺乏针对这些病毒的组织培养系统，因此大多根据它们的遗传亲缘关系来描述毒株。然而，由于缺乏统一的应用标准，导致了一系列令人困惑的菌株，不同的组为相似的遗传谱系使用了不同的名称。我们的目标是对NLV毒株之间的基因组关系进行结构化分析，试图为基因分型提供一个临时框架。我们组装了一个由31个潜在不同的基因组组I(GGI)和基因组II(GGII)NLV组成的小组，这些NLV反映了我们实验室检测到的菌株和已发表的序列中的多样性。为了研究基因组关系，对开放阅读框(ORF)1、2和3区域的序列进行了系统发育分析。根据编码衣壳蛋白N-末端的ORF2区域中80%以上的核苷酸同源性，以及无论使用何种方法，都具有一致的聚类性和较高的Bootstrap值，所测得的毒株在GGI中分为7个系统发育组，在GGII中至少分为5个系统发育组。对ORF1和ORF3区域的分析支持大多数菌株对ORF2来源的菌株所建立的聚类。在大多数实验室用于诊断RT-PCR的ORF1区域，当GGI中病毒的假定基因边界被设置为15%的核苷酸错配时，GGII中的病毒被设置为10%的核苷酸错配时，聚集性是一致的。根据ORF1和ORF2将两个菌株归入不同的集群，表明可能发生了重组。我们讨论了这些观察结果对NLV的分类和类型的影响。
Genomic characterization of Norwalk-like human caliciviruses (NLVs) originating from outbreaks and sporadic cases of acute gastroenteritis has revealed surprisingly high levels of diversity, even in the RNA polymerase gene, which is anticipated to be highly conserved. Since information on antigenic relationship is limited, due to the lack of a tissue culture system for these viruses, strains mostly are described on the basis of their genetic relatedness. However, the lack of uniformly applied criteria has led to a confusing array of strains with different groups employing different names for similar genetic lineages. Our goal was to conduct a structured analysis of genomic relationships among NLV strains in an attempt to provide an interim framework for genotyping. We assembled a panel of 31 potentially distinct genogroup I (GGI) and genogroup II (GGII) NLVs that reflected the diversity seen in strains detected by our laboratories and in published sequences. Phylogenetic analysis of sequences from regions of the open reading frames (ORF) 1, 2 and 3 was performed in order to investigate genomic relationships. The strains sequenced fell into seven phylogenetic groups in GGI and at least five phylogenetic groups in GGII, based on greater than 80% nucleotide identity in the region of ORF2 encoding the N-terminus of the capsid protein, and consistent clustering with high bootstrap values irrespective of the method used. Analysis of the ORF1 and ORF3 regions supported for most strains the clustering as established for those derived from ORF2. In the ORF1 region, used by most laboratories for diagnostic RT-PCR, clustering was consistent when a putative genotype border was set at 15% nucleotide mismatches for viruses in GGI and at 10% for viruses in GGII. Two strains grouped within different clusters based on ORF1 and ORF2 indicating that recombination may have occurred. We discuss the implications of these observations for the classification and typing of NLVs.