RT-PCR/MALDI-TOF Diagnostic Target Performance Reflects Circulating SARS-CoV-2 Variant Diversity in New York City.
RT-PCR/MALDI-TOF Diagnostic Target Performance Reflects Circulating SARS-CoV-2 Variant Diversity in New York City.
复制标题
DOI：
10.1016/j.jmoldx.2022.04.003
复制
发表时间：
2022-07
影响因子：
4.1
通讯作者：
Mt Sinai PSP Study Grp
中科院分区：
文献类型：
--
作者：
Hernandez, Matthew M.;Banu, Radhika;Gonzalez-Reiche, Ana S.;Gray, Brandon;Shrestha, Paras;Cao, Liyong;Chen, Feng;Shi, Huanzhi;Hanna, Ayman;Ramirez, Juan David;van de Guchte, Adriana;Sebra, Robert;Gitman, Melissa R.;Nowak, Michael D.;Cordon-Cardo, Carlos;Schutzbank, Ted E.;Simon, Viviana;van Bakel, Harm;Sordillo, Emilia Mia;Paniz-Mondol, Alberto E.;Mt Sinai PSP Study Grp
随着严重急性呼吸综合征冠状病毒2 （SARS-CoV-2）继续传播，出现了多种令人担忧的变体。新的变异给诊断平台带来了挑战，因为序列多样性可以改变引物/探针结合位点（PBSs），导致假阴性结果。masarray SARS-CoV-2小组（Agena Bioscience）使用RT-PCR和质谱法检测跨N和ORF1ab基因的五个多重靶标。本研究使用2021年4月11日至2021年8月28日期间采集的256份sars - cov -2阳性标本数据集，通过配对测序数据评估目标性能。在这段时间内，N基因的两个靶点（N2和N3）的序列多样性最大。在N3脱落的标本中，69%携带α特异性A28095U多态性，该多态性与N3前向PBS存在3 '错配，相对于具有28095A的标本，目标脱落的风险增加（相对风险为20.02;95% CI, 11.36 ~ 35.72; P < 0.0001）。此外，在N2辍学的标本中，90%携带delta特异性G28916U多态性，该多态性与N2探针PBS产生3 '错配，增加了目标辍学风险（相对风险为11.92;95% CI， 8.17至14.06;P < 0.0001）。这些发现突出了MassARRAY SARS-CoV-2小组靶点结果在揭示循环病毒多样性方面的强大能力，并强调了多靶点设计在捕获关注变体方面的强大作用。
As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to circulate, multiple variants of concern have emerged. New variants pose challenges for diagnostic platforms because sequence diversity can alter primer/probe-binding sites (PBSs), causing false-negative results. The MassARRAY SARS-CoV-2 Panel (Agena Bioscience) uses RT-PCR and mass spectrometry to detect five multiplex targets across N and ORF1ab genes. Herein, we use a data set of 256 SARS-CoV-2–positive specimens collected between April 11, 2021, and August 28, 2021, to evaluate target performance with paired sequencing data. During this time frame, two targets in the N gene (N2 and N3) were subject to the greatest sequence diversity. In specimens with N3 dropout, 69% harbored the Alpha-specific A28095U polymorphism that introduces a 3′-mismatch to the N3 forward PBS and increases risk of target dropout relative to specimens with 28095A (relative risk, 20.02; 95% CI, 11.36 to 35.72; P < 0.0001). Furthermore, among specimens with N2 dropout, 90% harbored the Delta-specific G28916U polymorphism that creates a 3′-mismatch to the N2 probe PBS and increases target dropout risk (relative risk, 11.92; 95% CI, 8.17 to 14.06; P < 0.0001). These findings highlight the robust capability of MassARRAY SARS-CoV-2 Panel target results to reveal circulating virus diversity, and they underscore the power of multitarget design to capture variants of concern.
登录
查看更多内容
DOI：
10.3390/life11101015
发表时间：
2021-09-27
期刊：
Life (Basel, Switzerland)
影响因子：
--
作者：
Chaintoutis SC;Chassalevris T;Balaska S;Mouchtaropoulou E;Tsiolas G;Vlatakis I;Tychala A;Koutsioulis D;Argiriou A;Skoura L;Dovas CI
通讯作者：
Dovas CI
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
影响因子：
64.5
作者：
Liu C;Ginn HM;Dejnirattisai W;Supasa P;Wang B;Tuekprakhon A;Nutalai R;Zhou D;Mentzer AJ;Zhao Y;Duyvesteyn HME;López-Camacho C;Slon-Campos J;Walter TS;Skelly D;Johnson SA;Ritter TG;Mason C;Costa Clemens SA;Gomes Naveca F;Nascimento V;Nascimento F;Fernandes da Costa C;Resende PC;Pauvolid-Correa A;Siqueira MM;Dold C;Temperton N;Dong T;Pollard AJ;Knight JC;Crook D;Lambe T;Clutterbuck E;Bibi S;Flaxman A;Bittaye M;Belij-Rammerstorfer S;Gilbert SC;Malik T;Carroll MW;Klenerman P;Barnes E;Dunachie SJ;Baillie V;Serafin N;Ditse Z;Da Silva K;Paterson NG;Williams MA;Hall DR;Madhi S;Nunes MC;Goulder P;Fry EE;Mongkolsapaya J;Ren J;Stuart DI;Screaton GR
通讯作者：
Screaton GR
影响因子：
9.3
作者：
Lefever, Steve;Pattyn, Filip;Vandesompele, Jo
通讯作者：
Vandesompele, Jo
影响因子：
4.6
作者：
Ahberg, Christian D.;Manz, Andreas;Neuzil, Pavel
通讯作者：
Neuzil, Pavel