TY - JOUR AU - Obeid, Dalia Abdullah AU - Alsanea, Madain Saleh AU - Alnemari, Rawan Talal AU - Al-Qahtani, Ahmed Ali AU - Althawadi, Sahar Isa AU - Mutabagani, Maysoon Saleh AU - Almaghrabi, Reem Saad AU - Alhadheq, Faten Mohammed AU - Alahideb, Basma Mohammed AU - Alhamlan, Fatimah Saeed PY - 2021/12/31 Y2 - 2024/03/28 TI - SARS-CoV-2 genetic diversity and variants of concern in Saudi Arabia JF - The Journal of Infection in Developing Countries JA - J Infect Dev Ctries VL - 15 IS - 12 SE - Coronavirus Pandemic DO - 10.3855/jidc.15350 UR - https://www.jidc.org/index.php/journal/article/view/35044933 SP - 1782-1791 AB - <p>Introduction: In December 2019, a new severe acute respiratory syndrome coronavirus, SARS-CoV-2, emerged in China, causing coronavirus disease 2019. The present study investigated genetic profiles and variations of SARS-CoV-2 distributed in different regions of Saudi Arabia to begin to understand the pathogenesis and transmission of SARS-CoV-2 in this country and analyzed associations of these variations with host factors.</p><p>Methodology: In total, 774 SARS-CoV-2 genomic sequences obtained and annotated by the Global Initiative on Sharing All Influenza Data (GISAID) were captured and analyzed.</p><p>Results: The most common SARS-CoV-2 clades in Saudi Arabia were GH followed by O, GR, G, and S. Statistically significant associations were detected between clades and patient outcome. Age, as a host factor, was significantly associated with many variables, including virus geographical location, clade, and patient outcome. The most common variants detected were the NSP12_P323L mutation 94.9%, followed by the D614G mutation (76%) and the NS3_Q57H mutation (71.4%). The concerned variants B.1.1.7, B.1.351, and P.1 were not detected in our population. D614G was associated with higher morbidities than the wild-type virus, including higher rates of death and hospitalization. The NS3_Q57H mutation was the only variant associated with better patient outcome than the wild type. Risk of death was highest with the NSP12_P323L mutation (OR = 1.84; 95% CI = 0.37-9.30) and lowest with the NS3_Q57H mutation (OR = 0.43; 95% CI = 0.25-0.727).</p><p>Conclusions: SARS-CoV-2 has evolved uniquely and independently in Saudi Arabia. Our findings provide evidence to begin linking the evolutionary implications to host factors and their effects on the virus severity and transmission.</p> ER -