Whole-genome analysis and mutation pattern of SARS-CoV-2 during first and second wave outbreak in Gwangju, Republic of Korea

Abstract

To investigate the specific genomic features and mutation pattern, whole and near-complete SARS-CoV-2 genome sequences were analyzed. Clinical samples were collected from 18 COVID-19–positive patients and subjected to nucleic acid purification. Cell culture was performed to extract various SARS-CoV-2 isolates. Whole-genome analysis was performed using next-generation sequencing, and phylogenetic analyses were conducted to determine genetic diversity of the various SARS-CoV-2 isolates. The next-generation sequencing data identified 8 protein-coding regions with 17 mutated proteins. We identified 51 missense point mutations and deletions in 5′ and 3′ untranslated regions. The phylogenetic analysis revealed that V and GH are the dominant clades of SARS-CoV-2 circulating in the Gwangju region of South Korea. Moreover, statistical analysis confirmed a significant difference between viral load (P < 0.001) and number of mutations (P < 0.0001) in 2 mutually exclusive SARS-CoV-2 clades which indicates frequent genomic alterations in SARS-CoV-2 in patients with high viral load. Our results provide an in-depth analysis of SARS-COV-2 whole genome which we believe, can shed light in the understanding of SARS-COV-2 pathogenesis and mutation pattern which can aid in the development of prevention methods as well as future research into the pathogenesis of SARS-CoV-2 and therapeutic development.

Consensus insertion/deletions and amino acid variations of all coding and noncoding regions of the SARS-CoV-2 Omicron clades, including the XBB and BQ.1 lineages

“…Most reports on SARS-CoV-2 variants have emphasized changes in the spike protein [ 3 , 4 ]. However, examination of the whole genome is important for assessing the impact of mutations in subvariants [ 14 ].…”

Consensus insertion/deletions and amino acid variations of all coding and noncoding regions of the SARS-CoV-2 Omicron clades, including the XBB and BQ.1 lineages

“…Most papers on SARS-CoV-2 variants covered the spike of the virus [3,4]. For this objective, the examination of the whole genome is important to predict the overall impact of subvariants [14]. Some indels and polymorphic amino acids were speci c to Omicron.…”

SARS-CoV-2 ORF7a Mutation Found in BF.5 and BF.7 Sublineages Impacts Its Functions

“…The first one occurred in the most recent common ancestor (MRCA) of BF.5 subvariants and the second one occurred in the MRCA of BA.7.14 and BF.7.27 subvariants (Figure 1A). In addition, a different mutation in the 47th residue of ORF7a (H47N) was reported in South Korea early in 2020 [32]. It is noteworthy that H47Y mutation was also reported in SARS-CoV ORF7a [33].…”