Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation

IF 0.8 Q4 GENETICS & HEREDITY

Meta Gene Pub Date : 2021-12-01 DOI:10.1016/j.mgene.2021.100950

Sirwan M.A. Al-Jaf , Sherko S. Niranji , Zana H. Mahmood

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引用次数: 7

Abstract

A common mutation has occurred in the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), known as D614G (A23403G). There are discrepancies in the impact of this mutation on the virus's infectivity. Also, the whole genome sequencings are expensive and time-consuming. This study aims to develop three fast economical assays for prompt identifications of the D614G mutation including Taqman probe-based real-time reverse transcriptase polymerase chain reaction (rRT PCR), an amplification refractory mutation system (ARMS) RT and restriction fragment length polymorphism (RFLP), in nasopharyngeal swab samples. Both rRT and ARMS data showed G614 mutants indicated by the presence of HEX probe and 176 bp, respectively. Additionally, the results of the RFLP data and DNA sequencings confirmed the prevalence of the G614 mutants. These methods will be important, in epidemiological, reinfections and zoonotic aspects, through detecting the G614 mutant in retro-perspective samples to track its origins and future re-emergence of D614 wild type.

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快速、廉价的方法探索SARS CoV-2 D614G突变

严重急性呼吸综合征冠状病毒2 (SARS CoV-2)的刺突蛋白中发生了一种常见的突变，称为D614G (A23403G)。这种变异对病毒传染性的影响存在差异。此外，全基因组测序既昂贵又耗时。本研究旨在建立基于Taqman探针的实时逆转录酶聚合酶链反应(rRT - PCR)、扩增难解突变系统(ARMS) RT和限制性片段长度多态性(RFLP)三种快速经济的检测方法，以快速鉴定鼻咽拭子样本中的D614G突变。rRT和ARMS数据均显示存在HEX探针的G614个突变体和176 bp的突变体。此外，RFLP数据和DNA测序结果证实了G614突变体的流行。这些方法在流行病学、再感染和人畜共患病方面具有重要意义，可以通过对样本进行回顾性检测来追踪其起源和D614野生型的再次出现。

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来源期刊

Meta Gene Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

1.10

自引率

0.00%

发文量

期刊介绍： Meta Gene publishes meta-analysis, polymorphism and population study papers that are relevant to both human and non-human species. Examples include but are not limited to: (Relevant to human specimens): 1Meta-Analysis Papers - statistical reviews of the published literature of human genetic variation (typically linked to medical conditionals and/or congenital diseases) 2Genome Wide Association Studies (GWAS) - examination of large patient cohorts to identify common genetic factors that influence health and disease 3Human Genetics Papers - original studies describing new data on genetic variation in smaller patient populations 4Genetic Case Reports - short communications describing novel and in formative genetic mutations or chromosomal aberrations (e.g., probands) in very small demographic groups (e.g., family or unique ethnic group). (Relevant to non-human specimens): 1Small Genome Papers - Analysis of genetic variation in organelle genomes (e.g., mitochondrial DNA) 2Microbiota Papers - Analysis of microbiological variation through analysis of DNA sequencing in different biological environments 3Ecological Diversity Papers - Geographical distribution of genetic diversity of zoological or botanical species.