key: cord-0918977-tbvm5g0p
authors: Ma, Kewei; Chen, Jieliang
title: Omicron XE emerges as SARS-CoV-2 keeps evolving
date: 2022-04-18
journal: Innovation (N Y)
DOI: 10.1016/j.xinn.2022.100248
sha: 98daaefdd0c1a6ea49c5547a5d10ad2172102ca2
doc_id: 918977
cord_uid: tbvm5g0p

nan

was designated by the world health organization (WHO) as a variant of concern (VOC). The Omicron has been spreading rapidly than any other previous variants of SARS-CoV-2, and is currently the dominant variant worldwide that accounts for >95% of sequenced cases submitted to GISAID. Three subvariants of Omicron including BA.1, BA.2 and BA.3 were detected in varying proportion in different parts of the world within weeks. The BA.2 subvariant, known popularly as the 'stealth' Omicron, lacks a particular genetic signature that distinguishes it from the Delta variant, has been shown to be more transmissible than BA.1, and has quickly become the dominant strain in many countries. However, considering that numbers at the current stage were too small to be analyzed, the data might be biased. Further monitoring is required for detailed evaluation of the XE's growth rate and transmissibility.

The recombination site of the XE subvariant is located within nonstructural protein J o u r n a l P r e -p r o o f (NSP) 6 of the SARS-CoV-2 genome (nucleotide position 11,537) , 2 and thus, the XE contains BA.1 mutations for NSP1-6 and then BA.2 mutations for the remainder of the genome. Moreover, the XE includes three mutations that are not present in all BA.1 or BA.2 sequences (Figure 1 ), of which NSP3 C3241T and NSP 12 C14599T are synonymous mutations, and the amino acid mutation V1069I is located in NSP3 (papain-like protease) which is responsible for cleaving viral polyproteins during replication. The impact of these mutations on viral transmission, immune evasion and virulence remains to be investigated. 

To prepare for the newly emerging XE subvariant, we need to actively monitor for potentially increased transmissibility, mortality and resistance to vaccine-induced immunity and antiviral therapeutics. Notably, CoVs are a group of viruses that regularly jump species boundaries 1 While it is difficult to predict what the next variant of concern will be, it is clear to reduce the likelihood of emergence of new variants, particularly those of high virulence. To achieve this, continuously strengthening the immune barrier and reducing the possibility of infection and reinfection are essential. Although it has been clear that less viral replication occurs in vaccinated people as a whole group, which would strongly restrict the evolutionary and immune escape pathways accessible to SARS-CoV-2, unequal global vaccine coverage has long been a problem. Therefore, greater efforts should be made to boost vaccination rate, especially in high-risk groups.

Meanwhile, public health intervention strategies, such as mask wearing, hygiene and physical distancing, are still of great importance. 5 Moreover, the development of vaccines and antiviral drugs with improved efficacy and broader coverage is warranted by the pandemic threat from the emerging variants.

The mysterious origins of the Omicron variant of SARS-CoV-2

SARS-CoV-2 variants of concern and variants under investigation in England

After the pandemic: perspectives on the future trajectory of COVID-19

Comparative analysis of the risks of hospitalisation and death associated with SARS-CoV-2 omicron (B.1.1.529) and delta (B.1.617.2) variants in England: a cohort study

The changing epidemiology of SARS-CoV-2