Validation of reduced S-gene target performance and failure for rapid surveillance of SARS-CoV-2 variants.
Validation of reduced S-gene target performance and failure for rapid surveillance of SARS-CoV-2 variants.
复制标题
验证S-Gene目标性能降低和对SARS-COV-2变体快速监视的失败的验证。
DOI：
10.1371/journal.pone.0275150
复制
发表时间：
2022
期刊：
影响因子：
3.7
通讯作者：
Taitel, Michael S.
中科院分区：
文献类型：
--
作者：
Clark, Cyndi;Schrecker, Joshua;Hardison, Matthew;Taitel, Michael S.
引起新冠肺炎的SARS-CoV-2病毒有许多变种，能够迅速传播，导致严重疾病。及时监测新的变种对于有效的公共卫生应对至关重要。确保诊断和分子检测的可用性和可及性是这类监测的关键。这项研究利用了反转录聚合酶链式反应和新冠肺炎阳性患者样本的全基因组测序结果，这些样本是宙斯盾科学公司和沃尔格林制药公司合作获得的，沃尔格林制药公司已经在美国和波多黎各的约5,200个地点进行了850多万次新冠肺炎检测。SARS-CoV-2的病毒进化会导致S基因的突变，从而导致诊断聚合酶链式反应中S基因扩增减少或失败。这些异常被标记为S基因靶向性能降低和S基因靶向失败，是携带del69-70突变的变体的特征，如Alpha和Omicron(B.1.1.529，BA.1和BA.1.1)谱系。这一观察结果已得到全基因组测序的验证，并可在收集后24-48小时内完成诊断PCR检测后提供推定的谱系数据。积极监测聚合酶链式反应和测序结果的趋势，是确定病毒传播变化和新出现的变种的关键。这项研究表明，重组SGTP和SGTF可用于对SARS-CoV-2变异株的近实时跟踪和监测，并且优于单独使用SGTF，因为已知携带del69-70突变的Alpha和Omicron(B.1.1.529、BA.1和BA.1.1)谱系比例很大，并且观察到存在S基因扩增。采用新的工具和技术来诊断急性感染和加快识别新出现的变种对支持公共卫生至关重要。
SARS-CoV-2, the virus that causes COVID-19, has many variants capable of rapid transmission causing serious illness. Timely surveillance of new variants is essential for an effective public health response. Ensuring availability and access to diagnostic and molecular testing is key to this type of surveillance. This study utilized reverse transcription polymerase chain reaction (RT-PCR) and whole genome sequencing results from COVID-19-positive patient samples obtained through a collaboration between Aegis Sciences Corporation and Walgreens Pharmacy that has conducted more than 8.5 million COVID-19 tests at ~5,200 locations across the United States and Puerto Rico. Viral evolution of SARS-CoV-2 can lead to mutations in the S-gene that cause reduced or failed S-gene amplification in diagnostic PCR tests. These anomalies, labeled reduced S-gene target performance (rSGTP) and S-gene target failure (SGTF), are characteristic of variants carrying the del69-70 mutation, such as Alpha and Omicron (B.1.1.529, BA.1, and BA.1.1) lineages. This observation has been validated by whole genome sequencing and can provide presumptive lineage data following completion of diagnostic PCR testing in 24–48 hours from collection. Active surveillance of trends in PCR and sequencing results is key to the identification of changes in viral transmission and emerging variants. This study shows that rSGTP and SGTF can be utilized for near real-time tracking and surveillance of SARS-CoV-2 variants, and is superior to the use of SGTF alone due to the significant proportion of Alpha and Omicron (B.1.1.529, BA.1, and BA.1.1) lineages known to carry the del69-70 mutation and observed to have S-gene amplification. Adopting new tools and techniques to both diagnose acute infections and expedite identification of emerging variants is critical to supporting public health.
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DOI：
10.1016/s0140-6736(22)00017-4
发表时间：
2022-01-29
期刊：
Lancet (London, England)
影响因子：
--
作者：
Wolter N;Jassat W;Walaza S;Welch R;Moultrie H;Groome M;Amoako DG;Everatt J;Bhiman JN;Scheepers C;Tebeila N;Chiwandire N;du Plessis M;Govender N;Ismail A;Glass A;Mlisana K;Stevens W;Treurnicht FK;Makatini Z;Hsiao NY;Parboosing R;Wadula J;Hussey H;Davies MA;Boulle A;von Gottberg A;Cohen C
通讯作者：
Cohen C
DOI：
10.3390/diagnostics12020467
发表时间：
2022-02-11
期刊：
Diagnostics (Basel, Switzerland)
影响因子：
--
作者：
Caputo V;Calvino G;Strafella C;Termine A;Fabrizio C;Trastulli G;Ingrascì A;Peconi C;Bardini S;Rossini A;Salvia A;Borsellino G;Battistini L;Caltagirone C;Cascella R;Giardina E
通讯作者：
Giardina E
影响因子：
3.5
作者：
Anaclerio F;Ferrante R;Mandatori D;Antonucci I;Capanna M;Damiani V;Tomo PD;Ferrante R;Ranaudo M;De Laurenzi V;Stuppia L;De Fabritiis S
通讯作者：
De Fabritiis S
使用Spike基因靶功能数据数据，英格兰11月15日至2021年12月31日，增强了SARS-COV-2 OMICRON变体出现的流行病学监测。
DOI：
10.2807/1560-7917.es.2022.27.11.2200143
发表时间：
2022-03
期刊：
Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin
影响因子：
--
作者：
Blomquist PB;Bridgen J;Bray N;O'Connell AM;West D;Groves N;Gallagher E;Utsi L;Jarvis CI;Hardstaff JL;Byers C;Metelmann S;Simons D;Zaidi A;Twohig KA;Savagar B;Løchen A;Ryan C;Wrenn K;Saavedra-Campos M;Abedin Z;Florence I;Cleary P;Elson R;Vivancos R;Lake IR
通讯作者：
Lake IR
影响因子：
120.7
作者：
Accorsi, Emma K.;Britton, Amadea;Verani, Jennifer R.
通讯作者：
Verani, Jennifer R.