Omicron variant of SARS-CoV-2: Genomics, transmissibility, and responses to current COVID-19 vaccines

Abstract

Currently, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide as an Omicron variant. This variant is a heavily mutated virus and designated as a variant of concern by the World Health Organization (WHO). WHO cautioned that the Omicron variant of SARS-CoV-2 held a very high risk of infection, reigniting anxieties about the economy's recovery from the 2-year pandemic. The extensively mutated Omicron variant is likely to spread internationally, posing a high risk of infection surges with serious repercussions in some areas. According to preliminary data, the Omicron variant of SARS-CoV-2 has a higher risk of reinfection. On the other hand, whether the current COVID-19 vaccines could effectively resist the new strain is still under investigation. However, there is very limited information on the current situation of the Omicron variant, such as genomics, transmissibility, efficacy of vaccines, treatment, and management. This review focused on the genomics, transmission, and effectiveness of vaccines against the Omicron variant, which will be helpful for further investigation of a new variant of SARS-CoV-2.

Keywords: SARS coronavirus; coronavirus; disease control; immune responses; vaccines/vaccine strains; virus classification.

Figure 1

Five SARS‐CoV‐2 variants have different amino acid mutation locations on their S proteins. On this figure, red lines indicate the mutation locations on the S protein of SARS‐CoV‐2 at the specified positions. FP stands for fusion peptide, and pink color specifies HR2: heptapeptide repeat sequence 2, TM: transmembrane domain, which showed in sky shade, NTD: N‐terminal domain shown in yellow and green color denotes RBD: receptor‐binding domain

Figure 2

The total number of confirmed Omicron variant cases per country and the probability of identifying a case. The figure shows that South Africa sequences many more samples than any other African country, but slower than most Western countries. Additionally, returning a viral sequence might take up to 2 weeks in countries with technical competence. Thus reliable statistics on verified instances lag behind the actual situation. Cases detected using their variant qPCR test, which is rather fast and tests numerous genes, are considered sufficient for counting as an Omicron variant by Norway and Denmark, even before full sequencing. So, it can be said that the sequencing rate influences the probability of discovering a case