Whole-genome sequencing of SARS-CoV-2 Omicron variant strains isolated from pharyngeal swab samples in Shandong province

Abstract

Objective To conduct whole genome sequencing of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) Omicron variant strains isolated from patients of a coronavirus disease 2019 (COVID-19) epidemic in Shandong province for effective control of COVID-19 epidemic. MethodsHigh-throughput sequencing technology was used to sequence the whole genome of SARS-CoV-2 Omicron variant strains isolated from pharyngeal swab samples collected from four COVID-19 cases in a prefecture of Shandong province in April 2022. MEGA 7.0.14 software was adopted in homology and mutation analysis and evolutionary tree construction of the viral strains. ResultsThe whole genome sequences of the four SARS-CoV-2 variants have 99.76% – 99.77% homology with the reference strain Wuhan-hu-1, and they are all located in the BA.2 clade of Omicron variant on the evolutionary tree. The 4 sequences all had multiple genetic loci variations and deletions; of which, A28271T mutation caused the -3 nucleotide of N gene translation initiation region changing from A to T and the deletion of amino acid from 24 to 26 of S protein resulted in the loss of the potential binding motif PPAY25-28 of the WW domain. Conclusion Several gene site mutants occurred in SARS-CoV-2 Omicron variants and the mutants may associate with highly infectious and camouflage of the variants and mild clinical symptoms of the viral infection.

Keywords

• severe acute respiratory coronavirus virus 2
• omicron variant
• whole genome
• translation initiation region
• ww domain