Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples.
Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples.
复制标题
利用纳米孔测序直接从临床样品中获取病毒靶向序列的评估。
DOI：
10.3390/v12121358
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发表时间：
2020-11-27
期刊：
影响因子：
--
通讯作者：
Couto N
中科院分区：
文献类型：
--
作者：
Schuele L;Cassidy H;Lizarazo E;Strutzberg-Minder K;Schuetze S;Loebert S;Lambrecht C;Harlizius J;Friedrich AW;Peter S;Niesters HGM;Rossen JWA;Couto N
鸟枪式宏基因组测序（SMg）能够同时检测和表征人类、动物和环境样品中的病毒。然而，缺乏灵敏度仍然是一个挑战，可能导致检测和数据采集不佳，无法进行详细分析。为了提高灵敏度，我们在人和动物样本中评估了广泛的靶向序列捕获（TSC）面板（ViroCap）。此外，我们针对Oxford Nanopore MinION调整了TSC，并将性能与SMg方法进行了比较。Illumina NextSeq上的TSC充当金标准。总体而言，TSC显著增加了挑战性人类样本中的病毒读段计数，在MinION上使用TSC实现了最高的基因组覆盖率。TSC还提高了动物样本中临床相关病毒（如甲型流感病毒）的基因组覆盖率和测序深度。然而，SMg已被证明足以表征高度多样化的动物病毒组。MinION上的TSC与NextSeq相当，可以提供有价值的替代方案，提供更长的读取时间，便携性和更低的初始成本。开发新的病毒富集方法来检测和表征重要的人类和动物病毒对“一个健康倡议”至关重要。
Shotgun metagenomic sequencing (SMg) enables the simultaneous detection and characterization of viruses in human, animal and environmental samples. However, lack of sensitivity still poses a challenge and may lead to poor detection and data acquisition for detailed analysis. To improve sensitivity, we assessed a broad scope targeted sequence capture (TSC) panel (ViroCap) in both human and animal samples. Moreover, we adjusted TSC for the Oxford Nanopore MinION and compared the performance to an SMg approach. TSC on the Illumina NextSeq served as the gold standard. Overall, TSC increased the viral read count significantly in challenging human samples, with the highest genome coverage achieved using the TSC on the MinION. TSC also improved the genome coverage and sequencing depth in clinically relevant viruses in the animal samples, such as influenza A virus. However, SMg was shown to be adequate for characterizing a highly diverse animal virome. TSC on the MinION was comparable to the NextSeq and can provide a valuable alternative, offering longer reads, portability and lower initial cost. Developing new viral enrichment approaches to detect and characterize significant human and animal viruses is essential for the One Health Initiative.
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影响因子：
19
作者：
Fraaij, P. L. A.;Wildschut, E. D.;Koopmans, M. P.
通讯作者：
Koopmans, M. P.
影响因子：
3.8
作者：
Lau, Susanna K. P.;Woo, Patrick C. Y.;Yuen, Kwok-Yung
通讯作者：
Yuen, Kwok-Yung
影响因子：
158.5
作者：
Wilson, M. R.;Sample, H. A.;Chiu, C. Y.
通讯作者：
Chiu, C. Y.
影响因子：
4.6
作者：
Couto N;Schuele L;Raangs EC;Machado MP;Mendes CI;Jesus TF;Chlebowicz M;Rosema S;Ramirez M;Carriço JA;Autenrieth IB;Friedrich AW;Peter S;Rossen JW
通讯作者：
Rossen JW
DOI：
10.1016/s1473-3099(20)30562-4
发表时间：
2020-11
期刊：
The Lancet. Infectious diseases
影响因子：
--
作者：
Meredith LW;Hamilton WL;Warne B;Houldcroft CJ;Hosmillo M;Jahun AS;Curran MD;Parmar S;Caller LG;Caddy SL;Khokhar FA;Yakovleva A;Hall G;Feltwell T;Forrest S;Sridhar S;Weekes MP;Baker S;Brown N;Moore E;Popay A;Roddick I;Reacher M;Gouliouris T;Peacock SJ;Dougan G;Török ME;Goodfellow I
通讯作者：
Goodfellow I