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SARS-CoV-2 genetic diversity and variants of concern in Saudi Arabia.
Obeid, Dalia Abdullah; Alsanea, Madain Saleh; Alnemari, Rawan Talal; Al-Qahtani, Ahmed Ali; Althawadi, Sahar Isa; Mutabagani, Maysoon Saleh; Almaghrabi, Reem Saad; Alhadheq, Faten Mohammed; Alahideb, Basma Mohammed; Alhamlan, Fatimah Saeed.
  • Obeid DA; Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
  • Alsanea MS; Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
  • Alnemari RT; Department of infectious Genome, Public Health Authority, Riyadh, Saudi Arabia.
  • Al-Qahtani AA; Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
  • Althawadi SI; Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
  • Mutabagani MS; Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
  • Almaghrabi RS; Department of Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
  • Alhadheq FM; Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
  • Alahideb BM; Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
  • Alhamlan FS; Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia. falhamlan@kfshrc.edu.sa.
J Infect Dev Ctries ; 15(12): 1782-1791, 2021 12 31.
Article in English | MEDLINE | ID: covidwho-1636074
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study Topics: Variants Limits: Adult / Aged / Female / Humans / Male / Middle aged Country/Region as subject: Asia Language: English Journal: J Infect Dev Ctries Journal subject: Communicable Diseases Year: 2021 Document Type: Article Affiliation country: Jidc.15350

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study Topics: Variants Limits: Adult / Aged / Female / Humans / Male / Middle aged Country/Region as subject: Asia Language: English Journal: J Infect Dev Ctries Journal subject: Communicable Diseases Year: 2021 Document Type: Article Affiliation country: Jidc.15350