Ligation-based assay for variant typing without sequencing: Application to SARS-CoV-2 variants of concern.
Ligation-based assay for variant typing without sequencing: Application to SARS-CoV-2 variants of concern.
复制标题
DOI：
10.1111/irv.13083
复制
发表时间：
2023-01
影响因子：
4.4
通讯作者：
Haselton, Frederick R.
中科院分区：
文献类型：
--
作者：
Nelson, Dalton J.;Shilts, Meghan H.;Pakala, Suman B.;Das, Suman R.;Schmitz, Jonathan E.;Haselton, Frederick R.
COVID-19 患病率在整个大流行期间一直保持较高水平，并出现间歇性激增，这主要是由于遗传变异的出现，这表明需要更容易获得的菌株分型测序技术。开发了一种基于连接的分型测定，通过识别特征性单核苷酸多态性 (SNP) 的存在来检测严重急性呼吸综合征病毒 2 (SARS-CoV-2) 的已知变体。描述了将该策略扩展到具有感兴趣的 SNP 的新变异和替代疾病的一般原则。值得注意的是，该策略利用市售试剂进行测定准备，以及标准实时聚合酶链反应 (PCR) 仪器进行测定性能。该检测显示，相对于病毒基因组测序的金标准，对 88 个临床样本的 Alpha、Delta 和 Omicron 变体进行分类的综合灵敏度和特异性分别为 96.6% 和 99.5%。在人工鼻咽样本中，其平均检测限为 7.4× 104 个基因组拷贝/mL。如临床样本的序列比对所示，基于连接的策略在目标感兴趣区域存在额外多态性的情况下表现强劲。该测定证明了强大的变异分型的潜力，其性能可与下一代测序相媲美，而无需测序所需的时间延迟和资源。资源依赖性和普遍性的减少可以扩大对大流行病监测的变异分类信息的获取。
COVID‐19 prevalence has remained high throughout the pandemic with intermittent surges, due largely to the emergence of genetic variants, demonstrating the need for more accessible sequencing technologies for strain typing. A ligation‐based typing assay was developed to detect known variants of severe acute respiratory syndrome virus 2 (SARS‐CoV‐2) by identifying the presence of characteristic single‐nucleotide polymorphisms (SNPs). General principles for extending the strategy to new variants and alternate diseases with SNPs of interest are described. Of note, this strategy leverages commercially available reagents for assay preparation, as well as standard real‐time polymerase chain reaction (PCR) instrumentation for assay performance. The assay demonstrated a combined sensitivity and specificity of 96.6% and 99.5%, respectively, for the classification of 88 clinical samples of the Alpha, Delta, and Omicron variants relative to the gold standard of viral genome sequencing. It achieved an average limit of detection of 7.4 × 104 genome copies/mL in contrived nasopharyngeal samples. The ligation‐based strategy performed robustly in the presence of additional polymorphisms in the targeted regions of interest as shown by the sequence alignment of clinical samples. The assay demonstrates the potential for robust variant typing with performance comparable with next‐generation sequencing without the need for the time delays and resources required for sequencing. The reduced resource dependency and generalizability could expand access to variant classification information for pandemic surveillance.
登录
查看更多内容
SARS-COV-2血统的估计可传播和影响B.1.1.7在英国。
DOI：
10.1126/science.abg3055
发表时间：
2021-04-09
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Davies NG;Abbott S;Barnard RC;Jarvis CI;Kucharski AJ;Munday JD;Pearson CAB;Russell TW;Tully DC;Washburne AD;Wenseleers T;Gimma A;Waites W;Wong KLM;van Zandvoort K;Silverman JD;CMMID COVID-19 Working Group;COVID-19 Genomics UK (COG-UK) Consortium;Diaz-Ordaz K;Keogh R;Eggo RM;Funk S;Jit M;Atkins KE;Edmunds WJ
通讯作者：
Edmunds WJ
影响因子：
9.4
作者：
Beek, IA;Mahalanabis, M;Frenkel, LM
通讯作者：
Frenkel, LM
影响因子：
3.7
作者：
Chung HY;Jian MJ;Chang CK;Lin JC;Yeh KM;Chen CW;Hsieh SS;Hung KS;Tang SH;Perng CL;Chang FY;Wang CH;Shang HS
通讯作者：
Shang HS
影响因子：
14.9
作者：
Lohman GJ;Bauer RJ;Nichols NM;Mazzola L;Bybee J;Rivizzigno D;Cantin E;Evans TC Jr
通讯作者：
Evans TC Jr
影响因子：
6.8
作者：
Buchta, Christoph;Camp, Jeremy, V;Goerzer, Irene
通讯作者：
Goerzer, Irene