Ismail, GhadaAbdelghafar, HossamSeadawy, Mohamed GGad, Ahmed FAgeez, AmrElShafei, AhmedMohammed, Shereen SaeedAli, Marym SaiedEl‑Ashry, Marwa abd El‑Rasoul2022-05-222022-05-222022-05https://doi.org/10.1186/s43141-022-00352-1http://repository.msa.edu.eg/xmlui/handle/123456789/4951ScopusBackground: 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 variantsen-USOmicron variantEgypt21Kgenome analysisArticlehttps://doi.org/10.1186/s43141-022-00352-1