SARS-CoV-2 Omicron variant: Characteristics and prevention

Abstract

Coronavirus disease 2019 (COVID-19) has brought about a great threat to global public health. Recently, a new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant B.1.1.529 has been reported in South Africa and induced a rapid increase in COVID-19 cases. On November 24, 2021, B.1.1.529 named Omicron was designated as a variant under monitoring (VUM) by World Health Organization (WHO). Two days later, the Omicron variant was classified as a variant of concern (VOC). This variant harbors a high number of mutations, including 15 mutations in the receptor-binding domain (RBD) of spike. The Omicron variant also shares several mutations with the previous VOC Alpha, Beta, and Gamma variants, which immediately raised global concerns about viral transmissibility, pathogenicity, and immune evasion. Here we described the discovery and characteristics of the Omicron variant, compared the mutations of the spike in the five VOCs, and further raised possible strategies to prevent and overcome the prevalence of the Omicron variant.

FIGURE 1

Waves of Coronavirus disease 2019 (COVID‐19) epidemics recorded thus far in South Africa. (A) Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has caused three waves of epidemics in South Africa. The number of daily confirmed infection cases is plotted. Data were downloaded from the World Health Organization (WHO). (B) The number of estimated cases infected by the indicated variants of concern (VOCs) in South Africa. The original data were downloaded from global initiative on sharing all influenza data (GISAID)

FIGURE 2

Omicron is spreading faster than other variants of concern (VOCs) in South Africa. The full genomic sequences were downloaded from global initiative on sharing all influenza data (GISAID), and the original data were processed with a logistic function

FIGURE 3

The schematic diagram showing the spike mutations of five variants of concern (VOCs). The mutations, including substitutions, deletions, and insertions, are defined based on the data from covariants at address https://covariants.org (20I for Alpha, 20H for Beta, 20J for Gamma, 21A for Delta, and 21K for Omicron, respectively)

FIGURE 4

Landscape of spike mutations in the Delta (left) and Omicron (right) variants. The structures are depicted based on the cryo‐electron microscopy spike trimer structure of protein data bank (PDB) code 6VYB and the crystal RBD/ACE2 complex structure of PDB code 6LZG. One protomer of the spike trimer is highlighted in green and its receptor‐binding domain (RBD) in cyan. The bound angiotensin‐converting enzyme 2 (ACE2) receptor is colored magenta. The mutations defined based on covariants are labeled