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

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

doi:10.1016/j.mgene.2021.100950

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

Meta Gene. 2021 Dec:30:100950. doi: 10.1016/j.mgene.2021.100950. Epub 2021 Jul 18.

Authors

Sirwan M A Al-Jaf^{1

2}, Sherko S Niranji^{1

2}, Zana H Mahmood^{3

4}

Affiliations

¹ Department of Biology, College of Education, University of Garmian, Kurdistan Region, Iraq.
² Coronavirus Research and Identification Lab., University of Garmian, Kurdistan Region, Iraq.
³ Molecular Diagnostic Laboratory, Sulaimani Veterinary Directorate, Sulaimani, Kurdistan, Iraq.
⁴ Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK.

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.

Keywords: ARMS; ARMS, amplification refractory mutation system RT; D614G; D614G, Aspartate 614 mutated to Glycine; Mutation; RFLP; RFLP, restriction fragment length polymorphism; Real-time PCR; SARS CoV-2; SARS CoV-2, severe acute respiratory syndrome coronavirus 2.