Metagenomic Analyses of Viruses in Stool Samples from Children with Acute Flaccid Paralysis
Metagenomic Analyses of Viruses in Stool Samples from Children with Acute Flaccid Paralysis
复制标题
DOI：
10.1128/jvi.02301-08
复制
发表时间：
2009-05-01
影响因子：
5.4
通讯作者：
Delwart, Eric
中科院分区：
文献类型：
--
作者：
Victoria, Joseph G.;Kapoor, Amit;Delwart, Eric
我们分析了从35名南亚非脊髓灰质炎急性弛缓性麻痹（AFP）儿童收集的粪便样本中的病毒核酸。序列非依赖性逆转录和PCR扩增的captain保护的，核酸酶抗性的病毒核酸，其次是DNA测序和序列相似性搜索。有限的桑格测序（每个样品35至240个亚克隆）鉴定了每个样品平均1.4种不同的真核病毒，而焦磷酸测序产生了每个样品2.6种病毒。除噬菌体和植物病毒外，我们还检测到已知的肠道病毒，包括轮状病毒、腺病毒、小核糖核酸病毒和人类肠道病毒A种（HEV-A）至HEV-C，以及小核糖核酸病毒科的许多其他成员，包括双埃柯病毒、爱知病毒、鼻病毒和人类心脏病毒。与先前报道的病毒相比，具有最不同序列的病毒包括一种新的小核糖核酸病毒属的成员和四种新的病毒种（双链病毒科、野大卫病毒科和圆环病毒科以及博卡病毒属的成员）。对来自AFP患者的六名健康接触者的样本进行了类似的分析，也含有许多病毒，特别是HEV-C，包括一种潜在的新型肠道病毒基因型。确定本研究中在不同人口群体中确定的新基因型、种、属和潜在新病毒家族的患病率和致病性将需要对不同人口群体和患者群体进行进一步研究，现在这些病毒基因组的知识有助于进一步研究。
We analyzed viral nucleic acids in stool samples collected from 35 South Asian children with nonpolio acute flaccid paralysis (AFP). Sequence-independent reverse transcription and PCR amplification of capsid-protected, nuclease-resistant viral nucleic acids were followed by DNA sequencing and sequence similarity searches. Limited Sanger sequencing (35 to 240 subclones per sample) identified an average of 1.4 distinct eukaryotic viruses per sample, while pyrosequencing yielded 2.6 viruses per sample. In addition to bacteriophage and plant viruses, we detected known enteric viruses, including rotavirus, adenovirus, picobirnavirus, and human enterovirus species A (HEV-A) to HEV-C, as well as numerous other members of the Picornaviridae family, including parechovirus, Aichi virus, rhinovirus, and human cardiovirus. The viruses with the most divergent sequences relative to those of previously reported viruses included members of a novel Picornaviridae genus and four new viral species (members of the Dicistroviridae, Nodaviridae, and Circoviridae families and the Bocavirus genus). Samples from six healthy contacts of AFP patients were similarly analyzed and also contained numerous viruses, particularly HEV-C, including a potentially novel Enterovirus genotype. Determining the prevalences and pathogenicities of the novel genotypes, species, genera, and potential new viral families identified in this study in different demographic groups will require further studies with different demographic and patient groups, now facilitated by knowledge of these viral genomes.