SARS-CoV-2 whole-genome sequencing using reverse complement PCR: For easy, fast and accurate outbreak and variant analysis.
SARS-CoV-2 whole-genome sequencing using reverse complement PCR: For easy, fast and accurate outbreak and variant analysis.
复制标题
DOI：
10.1016/j.jcv.2021.104993
复制
发表时间：
2021-11
期刊：
影响因子：
--
通讯作者：
Melchers WJG
中科院分区：
文献类型：
--
作者：
Coolen JPM;Wolters F;Tostmann A;van Groningen LFJ;Bleeker-Rovers CP;Tan ECTH;van der Geest-Blankert N;Hautvast JLA;Hopman J;Wertheim HFL;Rahamat-Langendoen JC;Storch M;Melchers WJG
在SARS-CoV-2大流行期间，出现了影响传播和疫苗有效性的突变报告。使用快速SARS-CoV-2全基因组测序（WGS）进行大规模突变分析通常是不可用的，但可以支持公共卫生组织和医院监测突变菌株的传播和不断上升的水平。在这里，我们报告了一种新的SARS-CoV-2 WGS技术，EasySeq™RC-PCR SARS-CoV-2 WGS试剂盒。通过逆行补体聚合酶链反应（RC-PCR），在单次PCR中获得Illumina文库，从而节省了时间和资源，便于高通量筛选。利用这种WGS技术，我们评估了2020年期间内梅亨大学医学中心173名患者和医护人员（HCW）中SARS-CoV-2的多样性和可能的传播。由于出现了令人关注的变体，我们在2021年筛选了SARS-CoV-2阳性样本，以确定突变和谱系。与目前的方法相比，使用EasySeq™RC-PCR SARS-CoV-2 WGS试剂盒，我们能够获得可靠的结果，以确认爆发集群，并额外识别以前不相关的新链接。此外，在样品中检测到各种感兴趣的SARS-CoV-2变体，并通过牛津纳米孔测序扩增子策略进行验证，这表明该技术适用于监测和监测当前流行的变体。
During the course of the SARS-CoV-2 pandemic reports of mutations with effects on spreading and vaccine effectiveness emerged. Large scale mutation analysis using rapid SARS-CoV-2 Whole Genome Sequencing (WGS) is often unavailable but could support public health organizations and hospitals in monitoring transmission and rising levels of mutant strains. Here we report a novel WGS technique for SARS-CoV-2, the EasySeq™ RC-PCR SARS-CoV-2 WGS kit. By applying a reverse complement polymerase chain reaction (RC-PCR), an Illumina library preparation is obtained in a single PCR, thereby saving time, resources and facilitating high-throughput screening. Using this WGS technique, we evaluated SARS-CoV-2 diversity and possible transmission within a group of 173 patients and healthcare workers (HCW) of the Radboud university medical center during 2020. Due to the emergence of variants of concern, we screened SARS-CoV-2 positive samples in 2021 for identification of mutations and lineages. With use of EasySeq™ RC-PCR SARS-CoV-2 WGS kit we were able to obtain reliable results to confirm outbreak clusters and additionally identify new previously unassociated links in a considerably easier workaround compared to current methods. Furthermore, various SARS-CoV-2 variants of interest were detected among samples and validated against an Oxford Nanopore sequencing amplicon strategy which illustrates this technique is suitable for surveillance and monitoring current circulating variants.
登录
查看更多内容
DOI：
10.1093/bioinformatics/btq224
发表时间：
2010-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Katoh K;Toh H
通讯作者：
Toh H
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
SARS-CoV-2 的全基因组测序：调整 Illumina 协议，在大流行期间快速准确地开展疫情调查
影响因子：
3.5
作者：
Pillay, Sureshnee;Giandhari, Jennifer;de Oliveira, Tulio
通讯作者：
de Oliveira, Tulio
影响因子：
5.8
作者：
Dona, Malathi S. I.;Prendergast, Luke A.;Salim, Agus
通讯作者：
Salim, Agus
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