Background: Several SARS-CoV-2 variants with increased transmissibility and/or potential immune escape have
emerged and rapidly spread worldwide. Ongoing surveillance analyses are performed worldwide to designate new
variants of concern (VOC) of coronavirus.
Main text: This report identifes the frst Egyptian patient with a confrmed SARS-CoV-2 omicron variant. The patient
showed positivity on reverse transcriptase-polymerase chain reaction and full genome sequencing was performed
to confrm the variant. The mutations found in the variant were compared with the GISAID reference strain hCoV-19/
Wuhan/WIV04/2019. Genome BLAST showed the highest similarity to omicron variants isolated in South Africa. Phylo‑
genetic analysis revealed that the variant belongs to the 21K clade.
Conclusions: The study indicates the importance of information-sharing among global public health partners.
Moreover the importance of implementation of full genome sequencing to rapidly identify and track the new SARS-
CoV-2 variants
