Open AccessSARS-CoV-2 genetic diversity and variants of concern in Saudi Arabia
Author(s) -
Dalia Obeid,
Madain Alsanea,
Rawan Talal Alnemari,
Ahmed AlQahtani,
Sahar Althawadi,
Maysoon S. Mutabagani,
Reem S. Almaghrabi,
Faten Mohammed Alhadheq,
Basma M. Alahideb,
Fatimah S. Alhamlan
Publication year - 2021
Publication title -
journal of infection in developing countries
Language(s) - English
Resource type - Journals
eISSN - 2036-6590
pISSN - 1972-2680
DOI - 10.3855/jidc.15350
Subject(s) - mutation , clade , biology , genetic diversity , virus , population , covid-19 , virology , genetic variation , mutation rate , genetics , disease , medicine , gene , phylogenetics , environmental health , infectious disease (medical specialty)
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.