Sub-lineages of the SARS-CoV-2 Omicron variants: Characteristics and prevention

Abstract

Since the start of the coronavirus disease 2019 (COVID-19) pandemic, new variants of severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) have emerged, accelerating the spread of the virus. Omicron was defined by the World Health Organization in November 2021 as the fifth "variant of concern" after Alpha, Beta, Gamma, and Delta. In recent months, Omicron has become the main epidemic strain. Studies have shown that Omicron carries more mutations than Alpha, Beta, Gamma, Delta, and wild-type, facilitating immune escape and accelerating its transmission. This review focuses on the Omicron variant's origin, transmission, main biological features, subvariants, mutations, immune escape, vaccination, and detection methods. We also discuss the appropriate preventive and therapeutic measures that should be taken to address the new challenges posed by the Omicron variant. This review is valuable to guide the surveillance, prevention, and development of vaccines and other therapies for Omicron variants. It is desirable to develop a more efficient vaccine against the Omicron variant and take more effective measures to constrain the spread of the epidemic and promote public health.

Keywords: Omicron variant; SARS‐CoV‐2; immune escape; neutralizing antibodies; vaccination.

FIGURE 1

Main areas ravaged by Omicron. As of July 22, 2022, the Omicron variant has been detected in at least 187 countries and 50 US states. (https://outbreak.info/situation‐reports/omicron?loc = ZAF&loc = GBR&loc = USA&selected = Worldwide&overlay = false [July 22, 2022])

FIGURE 2

Mutations in Spike protein of seven Omicron subvariants. Schematic shows the locations of amino acid substitutions of seven Omicron subvariants (BA.1, BA.2, BA.1.1, BA.3, BA.2.12.1, BA.4, and BA.5) in spike protein. The RBD and RBM region is shown in shallow violet red and deep violet red respectively, and the N‐terminal domain (NTD) region is demonstrated in bluish violet. (The figure was drawn on “Adobe illustrator” tool)

FIGURE 3

Resistance of individual mutations from Omicron spike protein to five types of antibodies (class 1, class 2, class 3, class 4, and NTD mAbs). The degree of resistance is represented by different colors. Resistance from strong to weak is indicated by red, orange, and yellow, respectively, while those favorable to antibody binding were blue. If the resistance strength is not marked, it indicates that there is little change in resistance to the antibody after the individual mutation. Mutations with strong resistance to NTD mAbs are G142D, Del143‐145, N211I, S477N, and N501Y; mutations with robust impedance to class 2 antibody are E484A and Q943R; L981F showed well binding ability to class 1 and class 3 antibodies. (The figure was drawn on “Adobe illustrator” tool)