key: cord-0952083-edknkvlj
authors: Majumdar, Swagata; Sarkar, Rakesh
title: Mutational and phylogenetic analyses of the two lineages of the Omicron variant
date: 2022-01-07
journal: J Med Virol
DOI: 10.1002/jmv.27558
sha: a4fc17fa7d7badfd096713d347d47e123355b2f6
doc_id: 952083
cord_uid: edknkvlj

Based on the recommendation of the WHO's Technical Advisory Group on Virus Evolution, WHO designated the variant B.1.1.529 as Variant of Concern (VOC) and named Omicron on 26 November 2021. This article is protected by copyright. All rights reserved.

Preliminary evidence indicated that Omicron has increased infectivity and a high transmission rate compared to Delta. [13] [14] [15] However, whether the rapid spread of Omicron in countries with increased population immunity is due to increased transmissibility and/or immune evasion remains unclear. Though, some recent studies have claimed the immune evasion properties of the Omicron. 14-17 Based on this existing evidence, Omicron is anticipated to overtake Delta in areas where community transmission occurs. The severity of Omicron infection still remains elusive. Preliminary studies from South Africa suggested that Omicron may be less severe than Delta, 18 and all COVID-19 patients, infected with Omicron, from countries of EU and EEA either showed mild symptoms or were asymptomatic. 19 Detection accuracy of routinely used PCR and antigen-based rapid diagnostic test (Ag-RDT) assays was not found to be influenced by most of the Omicron strains. However, the BA.1 lineage showed S gene target failure (SGTF) in RT-PCR assay due to multiple deletions in the NTD of S glycoprotein, whereas BA.2 lineage may skip SGTF due to lack of deletions in the NTD. Overall, the global threat related to Omicron remains very high for its potential to escape humoral immune response and high transmissibility, which may lead to another wave of COVID-19 with severe consequences. 19 F I G U R E 1 Phylogenetic analysis of the Omicron variant by Ultrafast Sample placement of Existing tRee (UShER). The phylogenetic tree (unrooted tree) was constructed with a total of 2012 SARS-CoV-2 strains involving 12 strains of the Omicron variant (red color) and 2000 strains from 25 different clades. Each color in the tree is representing a different clade/lineage

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