Rapid PCR-Based Nanopore Adaptive Sequencing Improves Sensitivity and Timeliness of Viral Clinical Detection and Genome Surveillance.
Rapid PCR-Based Nanopore Adaptive Sequencing Improves Sensitivity and Timeliness of Viral Clinical Detection and Genome Surveillance.
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DOI：
10.3389/fmicb.2022.929241
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发表时间：
2022
影响因子：
5.2
通讯作者：
中科院分区：
文献类型：
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作者：
纳米孔测序已被广泛应用于便携式Minion病原体的实时检测和监测。纳米孔自适应测序无需额外的前处理即可丰富靶上序列。在这项研究中，评估了自适应测序的性能，用于临床呼吸道样本的病毒基因组浓缩。采用基于连接的纳米孔自适应测序(LNAs)和基于快速聚合酶链式反应(PCR)的纳米孔自适应测序(RPNAS)工作流程，评估浓缩对人腺病毒(HAdV)暴发的鼻咽拭子样本的影响。进一步应用RPNAS检测鼻咽拭子标本中SARS冠状病毒2(SARS-CoV-2)，以评价其敏感性和及时性。RPNAs提高了HAdV样品的相对丰度(7.87-12.86倍)和数据产量(1.27-2.15倍)，而LNAs只增加了相对丰度，但对数据产量没有明显的富集性。与标准纳米孔测序相比，RPNAS从两个低丰度样本中检测到SARS-CoV-2读数，使SARS-CoV-2的覆盖率提高了36.68-98.92%，并缩短了达到相同覆盖率的时间。我们的研究强调了RPNAS用于直接从临床样本中浓缩病毒的实用价值，它具有更多的靶向数据和更短的测序时间来恢复病毒基因组。这些发现有望提高传染病快速识别和基因组监测的敏感度和及时性。
Nanopore sequencing has been widely used for the real-time detection and surveillance of pathogens with portable MinION. Nanopore adaptive sequencing can enrich on-target sequences without additional pretreatment. In this study, the performance of adaptive sequencing was evaluated for viral genome enrichment of clinical respiratory samples. Ligation-based nanopore adaptive sequencing (LNAS) and rapid PCR-based nanopore adaptive sequencing (RPNAS) workflows were performed to assess the effects of enrichment on nasopharyngeal swab samples from human adenovirus (HAdV) outbreaks. RPNAS was further applied for the enrichment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from nasopharyngeal swab samples to evaluate sensitivity and timeliness. The RPNAS increased both the relative abundance (7.87–12.86-fold) and data yield (1.27–2.15-fold) of HAdV samples, whereas the LNAS increased only the relative abundance but had no obvious enrichment on the data yield. Compared with standard nanopore sequencing, RPNAS detected the SARS-CoV-2 reads from two low-abundance samples, increased the coverage of SARS-CoV-2 by 36.68–98.92%, and reduced the time to achieve the same coverage. Our study highlights the utility of RPNAS for virus enrichment directly from clinical samples, with more on-target data and a shorter sequencing time to recover viral genomes. These findings promise to improve the sensitivity and timeliness of rapid identification and genomic surveillance of infectious diseases.
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DOI：
10.3390/v12121358
发表时间：
2020-11-27
期刊：
Viruses
影响因子：
--
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
通讯作者：
Couto N
影响因子：
12.3
作者：
Martin S;Heavens D;Lan Y;Horsfield S;Clark MD;Leggett RM
通讯作者：
Leggett RM
使用Oxford Nanopore的自适应测序评估人类阴道样品中微生物组富集和宿主DNA耗竭的评估。
影响因子：
4.6
作者：
Marquet M;Zöllkau J;Pastuschek J;Viehweger A;Schleußner E;Makarewicz O;Pletz MW;Ehricht R;Brandt C
通讯作者：
Brandt C
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
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng