The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first being identified in December 2019. The virus was responsible for massive human morbidity and mortality worldwide [1,2,3]. In late 2020, several SARS-CoV-2 “variants of concern” emerged that dictate special scrutiny. The new variants include the UK (UK) alpha variant (B.1.1.7), South Africa beta variant (B.1.351), Gamma (B.1.1.28.1), and Delta (B.1.617.2). The new variants have increased transmissibility and/or potential immune escape [4,5,6,7].

B.1.1.529 named Omicron variant, was first discovered in Botswana on November 11, 2021. South Africa reported it to the World Health Organization on November 24, 2021, and it was designated as a variant of concern (VOC) on November 26, 2021 [8]. As of 15 December 2021, the Omicron variant has already popped up in around 77 countries with the majority of the cases from the UK, South Africa, and the USA [9]. B.1.1.529 has 32 mutations on the spike protein in comparison with Delta variant (B.1.617.2) that had 9 mutations on the spike protein [10].

Ongoing surveillance analyses are performed worldwide to designate new variants of concern (VOC) of coronavirus. The surveillance is based upon utilizing RT-qPCR techniques for SARS-CoV-2 detection [11, 12], beside the use of next-generation sequencing (NGS) [13, 14]. The continuing surveillance gives the opportunity to track the SARS-CoV-2 genome evolution and variability. Moreover, the use of databases such as GISAID; (https://www.gisaid.org ) that elucidate its genomic characteristics, and Nextstrain; (https://nextstrain.org ) which monitors its spread within the global population.

This report reports the first omicron variant isolated in Egypt. The variant was verified by reverse transcriptase- polymerase chain reaction (RT-PCR), in addition to genomic sequencing and viral phylogenetic analysis.

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