Comparison of Algorithms for the Detection of Enteroviruses in Stool Specimens from Children Diagnosed with Acute Flaccid Paralysis

IF 16.4 1区化学 Q1 CHEMISTRY, MULTIDISCIPLINARY

Accounts of Chemical Research Pub Date : 2017-08-23 DOI:10.1101/179721

J. Adeniji, Funmilola A. Ayeni, Abdulfatah Ibrahim, Kazeem A. Tijani, Kazeem A. Tijani, T. Faleye, T. Faleye, M. Adewumi

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引用次数: 4

Abstract

With poliovirus eradication within reach, the WHO has included in its recommendations a cell-culture independent algorithm for enterovirus surveillance. This study was designed to compare both the cell culture dependent and independent algorithms and assess how either might impact our perception of the diversity of enterovirus types present in a sample. Sixteen paired samples (16 isolates from RD cell culture and their corresponding stool suspension. i.e. 32 samples) from AFP cases in Nigeria were analyzed in this study. One of these 16 sample pairs (the control) was previously identified and confirmed as poliovirus 2 (PV-2). All the samples were subjected to RNA extraction, cDNA synthesis, RT-snPCR (the WHO recommended cell-culture independent algorithm) and its modifications for co-infection detection and resolution. Amplicons were sequenced and strains identified using the enterovirus genotyping tool and phylogenetic analysis. The enterovirus diversity was shown to be the same between RD cell culture isolates and fecal suspension for the control and five (7, 10, 11, 12 & 14) of the samples analyzed. It was however, different for the remaining 10 (62.5%) samples analyzed. Fourteen different enterovirus types were identified in this study. To be precise, 9 (CV-B4, E6, E7, E13, E14, E19, E29, EV-B75 and EV-B77) and 5 (CV-A1, CV-A11, CV-A13, EV-C99 and PV2) EV-B and EV-C types, respectively where detected in this study. It is crucial to mention that E19 and EV-B75were only recovered from RD cell culture isolates while E14, EV-B77, CV-A11 and CV-A13 were only recovered from fecal suspension. The results of this study show that both the cell culture dependent and independent protocols recommended by the WHO for enterovirus detection unavoidably bias our perception of the diversity of enterovirus types present in a sample. Hence, rather than jettison one for the other, effort should be directed at harmonizing both for increased sensitivity.

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急性弛缓性麻痹患儿粪便中肠道病毒检测算法的比较

随着脊髓灰质炎病毒的根除指日可待，世卫组织在其建议中纳入了一种独立于细胞培养的肠道病毒监测算法。本研究旨在比较细胞培养依赖性和独立算法，并评估两者如何影响我们对样本中存在的肠道病毒类型多样性的感知。16个配对样本(16个分离自RD细胞培养及其相应的粪便悬浮液)。本研究分析了尼日利亚AFP病例的32个样本。这16对样本中有1对(对照)以前被鉴定并确认为2型脊髓灰质炎病毒(PV-2)。所有样本进行RNA提取、cDNA合成、RT-snPCR (WHO推荐的细胞培养不依赖算法)及其修改，以检测和解决共感染。利用肠道病毒基因分型工具和系统发育分析对扩增子进行测序和菌株鉴定。研究表明，在RD细胞培养分离物和作为对照的粪便悬浮液以及分析的5个样本(7、10、11、12和14)之间，肠道病毒的多样性是相同的。然而，其余10个(62.5%)样本的分析结果却不同。本研究鉴定出14种不同的肠道病毒类型。准确地说，本研究共检测到9种(CV-B4、E6、E7、E13、E14、E19、E29、EV-B75和EV-B77)和5种(CV-A1、CV-A11、CV-A13、EV-C99和PV2) EV-B和EV-C。值得一提的是，E19和ev - b75仅从RD细胞培养分离物中回收，而E14、EV-B77、CV-A11和CV-A13仅从粪便悬浮液中回收。本研究结果表明，世界卫生组织推荐的依赖细胞培养和独立的肠道病毒检测方案不可避免地会影响我们对样本中存在的肠道病毒类型多样性的看法。因此，与其为了另一个而抛弃一个，不如努力协调两者，以提高灵敏度。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Accounts of Chemical Research 化学-化学综合

CiteScore

31.40

自引率

1.10%

发文量

312

审稿时长

2 months

期刊介绍： Accounts of Chemical Research presents short, concise and critical articles offering easy-to-read overviews of basic research and applications in all areas of chemistry and biochemistry. These short reviews focus on research from the author’s own laboratory and are designed to teach the reader about a research project. In addition, Accounts of Chemical Research publishes commentaries that give an informed opinion on a current research problem. Special Issues online are devoted to a single topic of unusual activity and significance. Accounts of Chemical Research replaces the traditional article abstract with an article "Conspectus." These entries synopsize the research affording the reader a closer look at the content and significance of an article. Through this provision of a more detailed description of the article contents, the Conspectus enhances the article's discoverability by search engines and the exposure for the research.