Tracking the Genomic Evolution of SARS-CoV-2 for 29 Months in South Korea

Abstract

The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued, with the persistent emergence of variants of concern (VOCs). Therefore, this study aimed to track the genomic evolution of SARS-CoV-2 strains by sequencing the spike protein for 29 months, which accounted for the majority of the COVID-19 pandemic period. A total of 109 swabs from patients with confirmed coronavirus disease 2019 (COVID-19) infection were randomly collected between March 2020 and July 2022. After genomic sequencing, we analyzed the naming systems and phylogenetic trees. Five surge peaks of COVID-19 cases have been reported in South Korea, resulting in 14,000,000 cumulative confirmed cases and 17,000 deaths. Among the sequenced samples, 34 wild-type strains and 75 VOCs, including 4 Alpha, 33 Delta, 2 Epsilon, and 36 Omicron VOCs, were identified. Omicron strains were comprised of 8 BA.1.1 (21 K), 27 BA.2 (21 L), and 1 BA.2.12.1 (22C). Phylogenetic analysis of the identified isolates and representative sequences of SARS-CoV-2 strains revealed clusters that presented the WHO VOCs. Specific or unique mutations for each VOC waxed and waned according to the variant waves. Our findings allowed recognition of the overall trends of SARS-CoV-2 isolates, which implicated replication advantage, immune evasion, and disease management.

Evaluation of Long-Term Adaptive Immune Responses Specific to SARS-CoV-2: Effect of Various Vaccination and Omicron Exposure

“…Among the participants, 69 (88.5%) participants experienced breakthrough infections, and nine (11.5%) participants remained infection-naïve. Breakthrough infections were reported between January 2022 and January 2023, coinciding with the Omicron pandemic wave in South Korea [ 19 , 20 , 21 , 22 ]. Since all reported breakthrough infections occurred during the Omicron wave, these events were considered to be Omicron exposures.…”

Clinical performance of SARS-CoV-2 antigen-detection rapid diagnostic test using SERS-based lateral flow immunoassay

“…The variants of the virus is one of the crucial factors contributing to the false negative results of SARS-CoV-2 detection [ 44 ]. Given that the specimens were collected between August 2021 and May 2022, it could be inferred that the SARS-CoV-2 variants detected in this study were likely the Delta or Omicron (BA.1 and BA.2) variants, which were dominant during that period in Korea [ 45 ]. It is necessary to further compare the performance of ACROSIS according to the SARS-CoV-2 variants.…”

Humoral Response Kinetics and Cross-Immunity in Hospitalized Patients with SARS-CoV-2 WT, Delta, or Omicron Infections: A Comparison between Vaccinated and Unvaccinated Cohorts

“…The third wave spanned from 16 January 2022 to 23 July 2022, during which the Omicron variants, specifically BA.1 and sub-variant BA.2, circulated [ 16 ]. A previous study showed that each of these variants was almost exclusively predominant in South Korea during their respective time periods [ 3 , 17 ]. In this study, each predominant variant is hereafter referred to as wild type (WT), Delta, and Omicron, respectively.…”

“…While vaccines have proven effective in preventing COVID-19 and reducing the severity of illness, the virus has shown the ability to evolve and give rise to variants of concern (VOC). These variants harbor mutations in the spike protein or other viral components, allowing them to evade the immune response or enhance their transmissibility [ 1 , 3 , 4 ].…”