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

  • Dalia Abdullah Obeid Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia https://orcid.org/0000-0003-0251-1894
  • Madain Saleh Alsanea Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
  • Rawan Talal Alnemari Department of infectious Genome, Public Health Authority, Riyadh, Saudi Arabia
  • Ahmed Ali Al-Qahtani Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
  • Sahar Isa Althawadi Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
  • Maysoon Saleh Mutabagani Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
  • Reem Saad Almaghrabi Department of Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
  • Faten Mohammed Alhadheq Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
  • Basma Mohammed Alahideb Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
  • Fatimah Saeed Alhamlan Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
Keywords: SARS-CoV-2, COVID-19, Genome Variants, Genome

Abstract

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.

Author Biography

Fatimah Saeed Alhamlan, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia

Scientist at King Faisal Specialist Hospital and Research Center. Assistant Professor, College of Medicine, Alfaisal University. Majoring in Microbiology, Molecular Biology and Biochemistry (area of interest is Virology). 

Published
2021-12-31
How to Cite
1.
Obeid DA, Alsanea MS, Alnemari RT, Al-QahtaniAA, Althawadi SI, Mutabagani MS, Almaghrabi RS, Alhadheq FM, Alahideb BM, Alhamlan FS (2021) SARS-CoV-2 genetic diversity and variants of concern in Saudi Arabia. J Infect Dev Ctries 15:1782-1791. doi: 10.3855/jidc.15350
Section
Coronavirus Pandemic