Genome sequencing reveals existence of SARS-CoV-2 B.1.1.529 variant in Egypt.

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 identifies the first Egyptian patient with a confirmed SARS-CoV-2 omicron variant. The patient showed positivity on reverse transcriptase-polymerase chain reaction and full genome sequencing was performed to confirm 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. Phylogenetic 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.