2021-11-14

Laboratory of Molecular Biology and Cancer Immunology (Covid 19 Unit), Faculty of Science I, Lebanese University, Hadath, Beirut, 1003, Lebanon.; Research Department, Beirut Cardiac Institute, Old Airport Road, Beirut, Lebanon.; Bahman Hospital, Beirut, Lebanon.; Department of Microbiology and Parasitology, ISTUN Instituto de Salud Tropical, IdiSNA (Navarra Institute for Health Research), University of Navarra, c/ Irunlarrea 1, 31008, Pamplona, Navarra, Spain. panguewa@unav.es.; Laboratory of Molecular Biology and Cancer Immunology (Covid 19 Unit), Faculty of Science I, Lebanese University, Hadath, Beirut, 1003, Lebanon. kassem.hamze@ul.edu.lb.

BACKGROUND: The new SARS-CoV-2 variant VOC (202012/01), identified recently in the United Kingdom (UK), exhibits a higher transmissibility rate compared to other variants, and a reproductive number 0.4 higher. In the UK, scientists were able to identify the increase of this new variant through the rise of false negative results for the spike (S) target using a three-target RT-PCR assay (TaqPath kit). METHODS: To control and study the current coronavirus pandemic, it is important to develop a rapid and low-cost molecular test to identify the aforementioned variant. In this work, we designed primer sets specific to the VOC (202012/01) to be used by SYBR Green-based RT-PCR. These primers were specifically designed to confirm the deletion mutations Δ69/Δ70 in the spike and the Δ106/Δ107/Δ108 in the NSP6 gene. We studied 20 samples from positive patients, detected by using the Applied Biosystems TaqPath RT-PCR COVID-19 kit (Thermo Fisher Scientific, Waltham, USA) that included the ORF1ab