Diagnosing the novel SARS-CoV-2 by quantitative RT-PCR: variations and opportunities.
Diagnosing the novel SARS-CoV-2 by quantitative RT-PCR: variations and opportunities.
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DOI：
10.1007/s00109-020-01992-x
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发表时间：
2020-12
期刊：
影响因子：
--
通讯作者：
Benedito VA
中科院分区：
文献类型：
--
作者：
Barreto HG;de Pádua Milagres FA;de Araújo GC;Daúde MM;Benedito VA
世界目前正面临一场新型病毒大流行（SARS-CoV-2），大规模检测对于设计有效政策和控制战略以尽量减少其对全球人口的影响的决策至关重要。然而，检测病毒的存在是跟踪疾病传播的主要瓶颈。鉴于其对靶区域核苷酸序列的适应性，RT-qPCR是揭示新型病毒快速地理传播的有力盟友。我们评估了SARS-CoV-2诊断中的PCR变异，考虑了不同国家使用的公共基因组序列和诊断试剂盒。我们分析了2020年3月22日收集的样本中的226个SARS-CoV-2基因组序列。我们的工作利用了系统发育方法，揭示了病毒序列在地球仪传播时的早期进化，并为RT-qPCR引物和探针的设计提供了信息。一个国家在大流行期间迅速扩大检测能力，在很大程度上受到RNA分离和聚合酶链反应分析方面训练有素的人员以及硬件（热循环仪）的影响。我们建议，通过培训具有一定实验室经验的医疗和非医疗人员，如生物学相关研究生，快速的能力发展可以绕过这些瓶颈。此外，学术和商业实验室中使用的热循环仪可以及时校准和认证，以便在大流行期间正确进行检测。一个分散的、快速反应的培训和测试认证管道将使我们为管理未来的流行病做好更好的准备。本文的在线版本（10.1007/s 00109 -020-01992-x）包含补充材料，可供授权用户使用。
The world is currently facing a novel viral pandemic (SARS-CoV-2), and large-scale testing is central to decision-making for the design of effective policies and control strategies to minimize its impact on the global population. However, testing for the presence of the virus is a major bottleneck in tracking the spreading of the disease. Given its adaptability regarding the nucleotide sequence of target regions, RT-qPCR is a strong ally to reveal the rapid geographical spreading of novel viruses. We assessed PCR variations in the SARS-CoV-2 diagnosis taking into account public genome sequences and diagnosis kits used by different countries. We analyzed 226 SARS-CoV-2 genome sequences from samples collected by March 22, 2020. Our work utilizes a phylogenetic approach that reveals the early evolution of the virus sequence as it spreads around the globe and informs the design of RT-qPCR primers and probes. The quick expansion of testing capabilities of a country during a pandemic is largely impaired by the availability of adequately trained personnel on RNA isolation and PCR analysis, as well as the availability of hardware (thermocyclers). We propose that rapid capacity development can circumvent these bottlenecks by training medical and non-medical personnel with some laboratory experience, such as biology-related graduate students. Furthermore, the use of thermocyclers available in academic and commercial labs can be promptly calibrated and certified to properly conduct testing during a pandemic. A decentralized, fast-acting training and testing certification pipeline will better prepare us to manage future pandemics. The online version of this article (10.1007/s00109-020-01992-x) contains supplementary material, which is available to authorized users.
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DOI：
10.1016/j.jmoldx.2015.06.008
发表时间：
2015-11
期刊：
The Journal of molecular diagnostics : JMD
影响因子：
--
作者：
Chen H;Parimelalagan M;Lai YL;Lee KS;Koay ES;Hapuarachchi HC;Ng LC;Ho PS;Chu JJ
通讯作者：
Chu JJ
影响因子：
1.7
作者：
Abachin, Eric;Convers, Samantha;Nougarede, Nolwenn
通讯作者：
Nougarede, Nolwenn
影响因子：
2.2
作者：
Ambrose, Jason H.;Sekaran, Shamala Devi;Azizan, Azliyati
通讯作者：
Azizan, Azliyati
影响因子：
5.7
作者：
Huang, Wei E.;Lim, Boon;Cui, Zhanfeng
通讯作者：
Cui, Zhanfeng
影响因子：
10.7
作者：
Kumar, Sudhir;Stecher, Glen;Tamura, Koichiro
通讯作者：
Tamura, Koichiro