Genetic features of SARS-CoV-2 Alpha, Delta, and Omicron variants and their association with the clinical severity of COVID-19 in Vietnam

Le Van Nam; Trinh Cong Dien; Le Van Nguyen Bang; Pham Ngoc Thach; Le Van Duyet

doi:10.1016/j.ijregi.2024.03.003

Genetic features of SARS-CoV-2 Alpha, Delta, and Omicron variants and their association with the clinical severity of COVID-19 in Vietnam

IJID Reg. 2024 Mar 13:11:100348. doi: 10.1016/j.ijregi.2024.03.003. eCollection 2024 Jun.

Authors

Le Van Nam¹, Trinh Cong Dien¹, Le Van Nguyen Bang², Pham Ngoc Thach³, Le Van Duyet³

Affiliations

¹ Departments of Infectious Disease, Military Hospital, Hanoi, Vietnam.
² Luong The Vinh High School, Hanoi, Vietnam.
³ Micobiology and Molecular Biology Department, National Hospital for Tropical Diseases, Hanoi, Vietnam.

Abstract

Objectives: We investigated the genetic variations in the Alpha, Delta, and Omicron variants of SARS-CoV-2 and their association with clinical status and treatment outcomes in patients with COVID-19.

Methods: MiSeq was used to sequence the Alpha, Delta, and Omicron genomes, and MEGA 6.6 was used to define the nucleotide variations. We determined the association between clinical severity and treatment outcomes for the SARS-CoV-2 variants.

Results: The BA.1.1 and BA.2 lineages of the Omicron variant had 57-59 mutations, which is 2-2.7-fold higher than that of the B.1.1.7 (Alpha), B.1.617.2, and AY.57 (Delta) lineages. We found distinct mutations in SARS-CoV-2: five in Alpha (C26305T, G26558T, G7042T, C14120T, and C27509T); seven in Delta (C26408T, C1403T, C5184T, C9891T, T11418C, C11514T, and C22227T); and three in Omicron (C26408T, C8991T, and C25810T). Patients with the Delta variant had a severe rate of 23.8%, a critical rate of 53.7%, and a mortality rate of 38.9%, which were significantly higher than those with the Omicron and Alpha variants.

Conclusions: The Alpha, Delta, and Omicron variants in this study had genetic diversity and differed from the strains reported in other countries, with the Delta variant producing significantly more clinical severity and mortality than the Alpha and Omicron variants.

Keywords: Alpha variant; COVID-19; Delta variant; Disease severity; Omicron variant; SARS-COV-2.