Clinical Performance Characteristics of the Swift Normalase Amplicon Panel for Sensitive Recovery of Severe Acute Respiratory Syndrome Coronavirus 2 Genomes.
Clinical Performance Characteristics of the Swift Normalase Amplicon Panel for Sensitive Recovery of Severe Acute Respiratory Syndrome Coronavirus 2 Genomes.
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DOI：
10.1016/j.jmoldx.2022.05.007
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发表时间：
2022-09
影响因子：
4.1
通讯作者：
Roychoudhury, Pavitra
中科院分区：
文献类型：
--
作者：
Shrestha, Lasata;Lin, Michelle J.;Xie, Hong;Mills, Margaret G.;Bakhash, Shah A. Mohamed;Gaur, Vinod P.;Livingston, Robert J.;Castor, Jared;Bruce, Emily A.;Botten, Jason W.;Huang, Meei-Li;Jerome, Keith R.;Greninger, Alexander L.;Roychoudhury, Pavitra
基于扩增子的测序方法对于表征严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 的多样性、传播和进化至关重要，但需要对其临床实用性进行严格评估。在此，我们使用剩余的临床标本验证了 Swift Biosciences 的 SARS-CoV-2 Swift Normalase Amplicon Panel。从阳性样本中回收了符合我们既定文库和序列质量标准的高质量基因组，检测限为 40.08 个 SARS-CoV-2 拷贝/PCR，检测限为 95%。基因组恢复的广度通过一系列 CT 值（11.3 至 36.7；中位数 21.6）进行评估。在 428 个阳性样本中，413 个（96.5%）生成了未知碱基 <10% 的基因组，平均基因组覆盖度为 13,545×±SD 8382×。从 PCR 阴性样本 (n = 30) 或非 SARS-CoV-2 呼吸道病毒阳性样本 (n = 20) 中未回收到基因组。与全基因组鸟枪法宏基因组测序 (n = 14) 或刺突基因 Sanger 测序 (n = 11) 相比，所有情况下共有序列之间的成对同一性均为 100%，Swift 和鸟枪文库之间的等位基因频率高度一致 (R2 = 0.99)。当来自不同进化枝的样本以不同比例混合时，即使在 1:99 的混合物中也能检测到预期的变异。当部署为临床测试时，前 23 周内进行了 268 次测试，中位周转时间为 11 天，主要用于疫情调查和感染控制。
Amplicon-based sequencing methods are central in characterizing the diversity, transmission, and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but need to be rigorously assessed for clinical utility. Herein, we validated the Swift Biosciences' SARS-CoV-2 Swift Normalase Amplicon Panels using remnant clinical specimens. High-quality genomes meeting our established library and sequence quality criteria were recovered from positive specimens, with 95% limit of detection of 40.08 SARS-CoV-2 copies/PCR. Breadth of genome recovery was evaluated across a range of CT values (11.3 to 36.7; median, 21.6). Of 428 positive samples, 413 (96.5%) generated genomes with <10% unknown bases, with a mean genome coverage of 13,545× ± SD 8382×. No genomes were recovered from PCR-negative specimens (n = 30) or from specimens positive for non–SARS-CoV-2 respiratory viruses (n = 20). Compared with whole-genome shotgun metagenomic sequencing (n = 14) or Sanger sequencing for the spike gene (n = 11), pairwise identity between consensus sequences was 100% in all cases, with highly concordant allele frequencies (R2 = 0.99) between Swift and shotgun libraries. When samples from different clades were mixed at varying ratios, expected variants were detected even in 1:99 mixtures. When deployed as a clinical test, 268 tests were performed in the first 23 weeks, with a median turnaround time of 11 days, ordered primarily for outbreak investigations and infection control.
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影响因子：
16.6
作者：
Greaney AJ;Starr TN;Barnes CO;Weisblum Y;Schmidt F;Caskey M;Gaebler C;Cho A;Agudelo M;Finkin S;Wang Z;Poston D;Muecksch F;Hatziioannou T;Bieniasz PD;Robbiani DF;Nussenzweig MC;Bjorkman PJ;Bloom JD
通讯作者：
Bloom JD
影响因子：
64.5
作者：
Fauver, Joseph R.;Petrone, Mary E.;Grubaugh, Nathan D.
通讯作者：
Grubaugh, Nathan D.
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DOI：
10.1016/s1473-3099(21)00290-5
发表时间：
2021-11
期刊：
The Lancet. Infectious diseases
影响因子：
--
作者：
Bager P;Wohlfahrt J;Fonager J;Rasmussen M;Albertsen M;Michaelsen TY;Møller CH;Ethelberg S;Legarth R;Button MSF;Gubbels S;Voldstedlund M;Mølbak K;Skov RL;Fomsgaard A;Krause TG;Danish Covid-19 Genome Consortium
通讯作者：
Danish Covid-19 Genome Consortium
影响因子：
8.8
作者：
Degli-Angeli, Emily;Dragavon, Joan;Coombs, Robert W.
通讯作者：
Coombs, Robert W.
影响因子：
56.9
作者：
Deng, Xianding;Gu, Wei;Chiu, Charles Y.
通讯作者：
Chiu, Charles Y.