Delineation of Genomic Variants/Covariants of SARS-CoV-2, Their Frequencies, and Cooccurrence in Saudi Arabia in Context with Neighboring Countries

Background: Accumulating remarkable variations in spike-gene (Spk-gene) contribute to the evolution of potential spike (Spk)-variants and covariants of SARS-CoV-2 which influence prophylactic, diagnostic, and therapeutic countermeasures. Objective: The current research was designed to delineate the SARS-CoV-2 Spike-variant (Spk-variant) and SARS-CoV-2-Spike-covariant (Spk-covariant) frequencies and their cooccurrences in Saudi Arabia and the geographical regions around it. Methods: Relevant data (SARS-CoV-2-Spk-variant and SARS-CoV-2-Spk-covariants RNA-genome-sequences) offered by Bacterial and Viral Bioinformatics Resource Center (BV-BRC) was mined and retrieved using SARS-CoV-2-variants-tracker (real-time-based). Execution of comparative analysis of the data was accomplished using tidyverse/png/grid of the R-packages. Query datasets were generated for KSA and other neighboring regions and analyzed with cooccurrence and persistence network-clustering algorithms based on R-base-R packages and libraries. Data visualization was carried out by employing ggplot2/cooccurrence plots. Results: The substitution N501T, F157S, and H49Y in KSA, P681H in Iraq, and T478K in Bahrain were the most frequent variants. The Spk-variant-B.1, B.1.1.7, A.28, B.1.36 in KSA, CP.1, BA.2.75.2, BE.3, BM.1.1.3 in Qatar, XBB.1, EG.1in Kuwait, B. 1 in Jordan, B.1.1.7, B.1.428.1 in Iraq, and BA.1 and B.1.1.7 in Bahrain were the most frequent covariants. The Spk-variants (Spk-variant-N501Y and P681H) cooccurred in KSA and the majority of the neighboring countries (n = 6). Conclusion: The outcome of this research could be leveraged for deciding the appropriate prophylactic, diagnostic, and therapeutic countermeasures for the effective management of future outbreaks of disease in these regions