High-precision and cost-efficient sequencing for real-time COVID-19 surveillance.
High-precision and cost-efficient sequencing for real-time COVID-19 surveillance.
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DOI：
10.1038/s41598-021-93145-4
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发表时间：
2021-07-01
影响因子：
4.6
通讯作者：
Lee HY
中科院分区：
文献类型：
--
作者：
Park SY;Faraci G;Ward PM;Emerson JF;Lee HY
截至2020年9月，全球新冠肺炎病例已攀升至3300多万例，死亡总人数超过100万人。实时大规模的SARS-CoV-2全基因组测序是追踪传播链和估计疾病爆发来源的关键。然而，没有一种方法能够同时实现高精度、简单的工作流程和低成本。我们开发了一个用于新冠肺炎基因组监测的高精度、高性价比的SARS-CoV-2全基因组测序平台CorvGenSurv(冠状病毒基因组监测)。CorvGenSurv直接从新冠肺炎患者的鼻咽/口咽(NP/OP)拭子标本中扩增病毒RNA，并采用长读高通量测序方法将SARS-CoV-2全基因组分成三个片段进行测序。将整个基因组分成三个片段进行测序，大大减少了测序数据浪费，从而防止了基因组覆盖范围的缺失。我们通过对照基因组RNA测序和Sanger测序验证了我们的流水线的准确性。我们从2020年4月至6月在美国加利福尼亚州洛杉矶县新冠肺炎检测呈阳性的个人身上产生了近全长的全基因组序列。这些序列在G分支中高度多样化，有9个新的氨基酸突变，包括NSP12-M755I和ORF8-V117F。凭借其易于适应的设计，CorvGenSurv提供了广泛的基因组监测途径，使公共卫生能够立即对突发威胁做出反应。
COVID-19 global cases have climbed to more than 33 million, with over a million total deaths, as of September, 2020. Real-time massive SARS-CoV-2 whole genome sequencing is key to tracking chains of transmission and estimating the origin of disease outbreaks. Yet no methods have simultaneously achieved high precision, simple workflow, and low cost. We developed a high-precision, cost-efficient SARS-CoV-2 whole genome sequencing platform for COVID-19 genomic surveillance, CorvGenSurv (Coronavirus Genomic Surveillance). CorvGenSurv directly amplified viral RNA from COVID-19 patients’ Nasopharyngeal/Oropharyngeal (NP/OP) swab specimens and sequenced the SARS-CoV-2 whole genome in three segments by long-read, high-throughput sequencing. Sequencing of the whole genome in three segments significantly reduced sequencing data waste, thereby preventing dropouts in genome coverage. We validated the precision of our pipeline by both control genomic RNA sequencing and Sanger sequencing. We produced near full-length whole genome sequences from individuals who were COVID-19 test positive during April to June 2020 in Los Angeles County, California, USA. These sequences were highly diverse in the G clade with nine novel amino acid mutations including NSP12-M755I and ORF8-V117F. With its readily adaptable design, CorvGenSurv grants wide access to genomic surveillance, permitting immediate public health response to sudden threats.
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影响因子：
5.3
作者：
Arias A;Watson SJ;Asogun D;Tobin EA;Lu J;Phan MVT;Jah U;Wadoum REG;Meredith L;Thorne L;Caddy S;Tarawalie A;Langat P;Dudas G;Faria NR;Dellicour S;Kamara A;Kargbo B;Kamara BO;Gevao S;Cooper D;Newport M;Horby P;Dunning J;Sahr F;Brooks T;Simpson AJH;Groppelli E;Liu G;Mulakken N;Rhodes K;Akpablie J;Yoti Z;Lamunu M;Vitto E;Otim P;Owilli C;Boateng I;Okoror L;Omomoh E;Oyakhilome J;Omiunu R;Yemisis I;Adomeh D;Ehikhiametalor S;Akhilomen P;Aire C;Kurth A;Cook N;Baumann J;Gabriel M;Wölfel R;Di Caro A;Carroll MW;Günther S;Redd J;Naidoo D;Pybus OG;Rambaut A;Kellam P;Goodfellow I;Cotten M
通讯作者：
Cotten M
影响因子：
9.8
作者：
Kennedy DA;Read AF
通讯作者：
Read AF
影响因子：
56.9
作者：
Gonzalez-Reiche, Ana S.;Hernandez, Matthew M.;van Bakel, Harm
通讯作者：
van Bakel, Harm
DOI：
10.1038/gim.2017.211
发表时间：
2018-06
期刊：
Genetics in medicine : official journal of the American College of Medical Genetics
影响因子：
--
作者：
Khoury MJ;Bowen MS;Clyne M;Dotson WD;Gwinn ML;Green RF;Kolor K;Rodriguez JL;Wulf A;Yu W
通讯作者：
Yu W
影响因子：
56.9
作者：
Deng, Xianding;Gu, Wei;Chiu, Charles Y.
通讯作者：
Chiu, Charles Y.