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. 2022 May 11;20(1):70.
doi: 10.1186/s43141-022-00352-1.

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

Ghada Ismail  1   2 , Hossam Abdelghaffar  3   4 , Mohamed G Seadawy  5 , Mostafa F El-Hosseny  6 , Ahmed F Gad  6 , Amr Ageez  7 , Ahmed ElShafei  8 , Shereen Saeed Mohammed  2 , Marym Saied Ali  2 , Marwa Abd El-Rasoul El-Ashry  1
Affiliations

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

Ghada Ismail et al. J Genet Eng Biotechnol. .

Abstract

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.

Keywords: 21K; Egypt; Omicron variant; genome analysis.

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Conflict of interest statement

The authors declare no conflict of interest. The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Fig. 1
Fig. 1
A Phylogenetic analysis of the omicron variant isolated in this case report. The isolate (arrow) is grouped inside the 21K sequences of SARS-CoV-2 virus. B structural visualization of the spike glycoprotein with aa changes identified in the query sequences shown as colored balls. Spike glycoprotein (PDB: 6acj, EM 4.2 Angstrom) in complex with host cell receptor ACE2 (green ribbon). The variations displayed in structure (nearest residue if in loop/termini region): A67V H69del V70del(69) T95I G142D V143del Y144del(143) Y145del(143) N211del L212I ins214EPE G339D V367F S371L S373P S375F S477N T478K E484A Q493R G496S Q498R N501Y Y505H T547K D614G H655Y N679K(674) P681H(674) D796Y N856K Q954H N969K L981F
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