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

Ghada Ismail; Hossam Abdelghaffar; Mohamed G Seadawy; Mostafa F El-Hosseny; Ahmed F Gad; Amr Ageez; Ahmed ElShafei; Shereen Saeed Mohammed; Marym Saied Ali; Marwa Abd El-Rasoul El-Ashry

doi:10.1186/s43141-022-00352-1

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

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

Authors

Affiliations

¹ Clinical Pathology Department, Faculty of Medicine, Ain Shams University, Al-Abbasia PO11588, Cairo, Egypt.
² Reference Laboratory of the Egyptian University Hospitals (RLEUH), Cairo, Egypt.
³ Department of ENT, Faculty of Medicine, Helwan University, Helwan, Egypt.
⁴ Supreme Council for University Hospitals, Cairo, Egypt.
⁵ Biological Prevention Department, Chemical Warfare, 4.5 km Suez-Cairo Rd, Almaza, Cairo, Egypt. [email protected].
⁶ Biological Prevention Department, Chemical Warfare, 4.5 km Suez-Cairo Rd, Almaza, Cairo, Egypt.
⁷ Faculty of Biotechnology, MSA University, 6 October City, Egypt.
⁸ Theodor Belharz Research Institute, Warraq Al Hadar, Egypt.

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.