Ann Lab Med.  2023 Mar;43(2):211-213. 10.3343/alm.2023.43.2.211.

Rapid Emergence of the Omicron Variant of Severe Acute Respiratory Syndrome Coronavirus 2 in Korea

• Park AK
• Kim IH
• Lee CY
• Kim JA
• Lee H
• Kim HM
• Lee NJ
• Woo S
• Lee J
• Rhee J
• Yoo CK
• Kim EJ

• KMID: 2551701
• DOI: http://doi.org/10.3343/alm.2023.43.2.211

Figure

• 

  Fig. 1 Prevalence of SARS-CoV-2 variants in Korea. (A) Distribution of the Delta and Omicron variants of SARS-CoV-2 in Korea from November 15, 2021 to February 3, 2022. The number of daily reported cases is presented as a grey line. (B) Cumulative cases of four variants of concerns in Korea indexed by days. The Gamma variant has not been isolated from domestic cases in Korea. Abbreviation: SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

• 

  Fig. 2 Phylogenetic analysis of SARS-CoV-2 sequences. In total, 858 sequences, including 286 sequences from isolates from Korea, were used to construct the tree. All sequences were aligned to the Wuhan-Hu-1 reference sequence using Geneious Prime software (https://www.geneious.com/) and then manually trimmed to equal lengths. A maximum-likelihood phylogenetic tree was reconstructed using FastTree under the GRT+γ nucleotide substitution model, and the phylogenetic tree was visualized using iTOL (https://itol.embl.de/). Abbreviation: SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Reference

1. WHO. Classification of Omicron (B.1.1.529): SARS-CoV-2 variant of concern. https://www.who.int/news/item/26-11-2021-classification-of-omicron-(B.1.1.529)-sars-cov-2-variant-of-concern. Updated on Nov 2021.

2. Harvey WT, Carabelli AM, Jackson B, Gupta RK, Thomson EC, Harrison EM, et al. 2021; SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol. 19:409–24. DOI: 10.1038/s41579-021-00573-0. PMID: 34075212. PMCID: PMC8167834.

3. Alenquer M, Ferreira F, Lousa D, Valério M, Medina-Lopes M, Bergman ML, et al. 2021; Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. PLoS Pathog. 17:e1009772. DOI: 10.1371/journal.ppat.1009772. PMID: 34352039. PMCID: PMC8341613.

4. Shu Y, McCauley J. 2017; GISAID: Global initiative on sharing all influenza data - from vision to reality. Euro Surveill. 22:30494. DOI: 10.2807/1560-7917.ES.2017.22.13.30494. PMID: 28382917. PMCID: PMC5388101.

5. Park AK, Kim IH, Kim J, Kim JM, Kim HM, Lee CY, et al. 2021; Genomic surveillance of SARS-CoV-2: distribution of clades in the Republic of Korea in 2020. Osong Public Health Res Perspect. 12:37–43. DOI: 10.24171/j.phrp.2021.12.1.06. PMID: 33659153. PMCID: PMC7899228.

6. Park AK, Kim IH, Man Kim H, Lee H, Lee NJ, Kim JA, et al. 2022; SARS-CoV-2 B.1.619 and B.1.620 lineages, South Korea, 2021. Emerg Infect Dis. 28:415–9. DOI: 10.3201/eid2802.211653. PMID: 35076365. PMCID: PMC8798691.

7. Rambaut A, Holmes EC, Hill V, O'Toole Á, McCrone JT, Ruis C, et al. 2020; A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology. Nat Microbiol. 5:1403–7. DOI: 10.1038/s41564-020-0770-5. PMID: 32669681. PMCID: PMC7610519.

8. Kim EY, Choe YJ, Park H, Jeong H, Chung JH, Yu J, et al. 2022; Community transmission of SARS-CoV-2 Omicron variant, South Korea, 2021. Emerg Infect Dis. 28:898–900. DOI: 10.3201/eid2804.220006. PMID: 35171760. PMCID: PMC8962914.

9. Liu L, Iketani S, Guo Y, Chan JF, Wang M, Liu L, et al. 2022; Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2. Nature. 602:676–81. DOI: 10.1038/s41586-021-04388-0. PMID: 35016198.

10. Cao Y, Wang J, Jian F, Xiao T, Song W, Yisimayi A, et al. 2022; Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Nature. 602:657–63. DOI: 10.1038/s41586-021-04385-3. PMID: 35016194. PMCID: PMC8866119.