Genetic features of SARS-CoV-2 alpha, delta, and omicron variants and their association with the clinical severity of COVID-19 in Vietnam

Objectives We investigated 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 coronavirus disease 2019 (COVID-19). Methods MiSeq was used to sequence the alpha, delta, and omicron genomes, and MEGA 6.6 was used to define nucleotide variations. We determined the association between clinical severity and treatment outcomes for the SARS-CoV-2 variants. Results 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: 5 in alpha (C26305T, G26558T, G7042T, C14120T, and C27509T); 7 in delta (C26408T, C1403T, C5184T, C9891T, T11418C, C11514T, and C22227T); and 3 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 strains reported in other countries, with the delta variant producing significantly more clinical severity and mortality than the alpha and omicron variants.