Omicron SARS-CoV-2 variant: a new chapter in the COVID-19 pandemic

Abstract

On Nov 25, 2021, about 23 months since the first reported case of COVID-19 and after a global estimated 260 million cases and 5•2 million deaths, 1 a new SARS-CoV-2 variant of concern (VoC), omicron, 2 was reported. Omicron emerged in a COVID-19-weary world in which anger and frustration with the pandemic are rife amid widespread negative impacts on social, mental, and economic wellbeing. Although previous VoCs emerged in a world in which natural immunity from COVID-19 infections was common, this fifth VoC has emerged at a time when vaccine immunity is increasing in the world.The emergence of the alpha, beta, and delta SARS-CoV-2 VoCs were associated with new waves of infections, sometimes across the entire world. 3 For example, the increased transmissibility of the delta VoC was associated with, among others, a higher viral load, 4 longer duration of infectiousness, 5 and high rates of reinfection, because of its ability to escape from natural immunity, 6 which resulted in the delta VoC rapidly becoming the globally dominant variant. The delta VoC continues to drive new waves of infection and remains the dominant VoC during the fourth wave in many countries. Concerns about lower vaccine efficacy because of new variants have changed our understanding of the COVID-19 endgame, disabusing the world of the notion that global vaccination is by itself adequate for controlling SARS-CoV-2 infection. Indeed, VoCs have highlighted the importance of vaccination in combination with existing public health prevention measures, such as masks, as a pathway to viral endemicity. 7

Tracking and controlling the spatiotemporal spread of SARS-CoV-2 Omicron variant in South Africa

“…This variant contains >30 spike protein amino acid mutations that possibly are associated with increased transmissibility, severity, and capacity for immune escape [ [4] , [5] , [6] ]. It has been found that Omicron variant may lead to more significant escape from immune protection elicited by previous SARS-CoV-2 infection and perhaps even by existing Coronavirus disease 2019 (COVID-19) vaccines [ [7] , [8] , [9] , [10] ]. Thus, Omicron was designated as variant of concern (VOC), by the World Health Organization (WHO) on November 26th, 2021 [ 11 ].…”

Highly mutated SARS-CoV-2 Omicron variant sparks significant concern among global experts – What is known so far?

“…These amino acid substitutions occur in the Receptor Binding Domain (RBD). Interestingly, this variant carries mutations found in other variants of concern (VOC); it has the deletion at spike position 69–70, similar to the Alpha variant that leads to the S gene dropout or S gene target failure [ 8 ]. It also has three key mutations similar to those found in Beta and Gamma variants that confer immune escape [ 8 ].…”

“…Interestingly, this variant carries mutations found in other variants of concern (VOC); it has the deletion at spike position 69–70, similar to the Alpha variant that leads to the S gene dropout or S gene target failure [ 8 ]. It also has three key mutations similar to those found in Beta and Gamma variants that confer immune escape [ 8 ]. Additionally, it has a range of close mutations to the furin cleavage site similar to those present in the Delta variant [ 8 ].…”

“…It also has three key mutations similar to those found in Beta and Gamma variants that confer immune escape [ 8 ]. Additionally, it has a range of close mutations to the furin cleavage site similar to those present in the Delta variant [ 8 ]. Based on these mutations, it is thought that the Omicron variant may have similar characteristics to all other variants, at least at the molecular level [ 8 ].…”

“…Based on the report from the physicians and primary care providers in South Africa, it is known that the clinical presentation is similar to other COVID-19 variants. However, the severity of the cases will be more apparent in the coming days [ 8 ]. Initially, identified individuals affected in South Africa were cohorts of young university students with mild symptoms, including fatigue [ 9 ].…”