In silico analysis for SARS-CoV-2 detection in the context of genetic variability of the Algerian omicron variant.

Abstract

The risk to public health conferred by the Omicron variant is still not completely clear, although its numerous gene mutations have raised concerns regarding its potential for increased transmissibility and immune escape. In this study, we test the compatibility of the different primers and probes available in different commercial kits sold internationally with all the sequences of SARS-CoV-2 analyzed in Algeria until March 2023. The Algerian SARS-CoV-2 Omicron variant sequences were aligned with the Muscle tool using Genious software. We also used primers and probes sequences of seven international RT-qPCR kits; CDC China, Charite Germany, HKU Hong Kong, NIH Thailand, NIID Japan, CDC US, and Pasteur Institute. We used the primer check v2.0 developed by VIROSCIENCE LAB, To identify the different mutations located at the level of primers and probes about the Algerian sequences of SARS-CoV2. Statistical tests were carried out by calculating the $x^2$ test. We found regarding the Forward primer sequences that the two Thailand and Japan kits are less specific to the Algerian version of the SARS-CoV-2 Omicron variant genome compared to the other kits (p=10^-6). Furthermore, regarding the Reverse primers and fluorescent Probes, the three kits; Thailand, Japan, and CDC US; are less effective (p=10^-6). Regarding all primers and probes, this work allowed us to conclude that the four RT-qPCR kits: CDC China, Charite Germany, NHD Hong Kong, and Pasteur Institute seem to be more specific for the Algerian omicron genome detection and therefore for diagnosis of COVID-19 in Algeria.