Journal Article

SARS-CoV-2 genetic diversity and variants of concern in Saudi Arabia

Almaghrabi, Reem Saad, Alnemari, Rawan Talal, Alhadheq, Faten Mohammed, Alhamlan, Fatimah Saeed, Obeid, Dalia Abdullah, Alahideb, Basma Mohammed, Mutabagani, Maysoon Saleh, Althawadi, Sahar Isa, Alsanea, Madain Saleh, Al-Qahtani, Ahmed Ali

2021

Overview

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. 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. 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). 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.

• Publisher: Journal of Infection in Developing Countries,The Journal of Infection in Developing Countries
• Subject: Adult / Aged / Clinical outcomes / Coronaviruses / COVID-19 / COVID-19 - epidemiology / COVID-19 - genetics / COVID-19 - transmission / Disease transmission / Female / Genome / Genome Variants / Genome, Viral / Hospitalization - statistics & numerical data / Humans / Male / Middle Aged / Mutation / Mutation - genetics / Pandemics / SARS-CoV-2 / Saudi Arabia - epidemiology / Severe acute respiratory syndrome coronavirus 2 / Whole Genome Sequencing