基因组测序显示埃及存在新冠病毒B.1.1.529变种。

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

作者信息

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

机构信息

Clinical Pathology Department, Faculty of Medicine, Ain Shams University, Al-Abbasia PO11588, Cairo, Egypt.

Reference Laboratory of the Egyptian University Hospitals (RLEUH), Cairo, Egypt.

出版信息

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

DOI:10.1186/s43141-022-00352-1

PMID:35543892

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9092035/

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.

摘要

背景

几种具有更高传播性和/或潜在免疫逃逸能力的严重急性呼吸综合征冠状病毒2（SARS-CoV-2）变体已经出现并在全球迅速传播。全球正在进行监测分析，以指定冠状病毒新的关注变体（VOC）。

正文

本报告确定了首例确诊感染SARS-CoV-2奥密克戎变体的埃及患者。该患者逆转录聚合酶链反应呈阳性，并进行了全基因组测序以确认该变体。将该变体中发现的突变与全球共享流感数据倡议组织（GISAID）的参考毒株hCoV-19/武汉/WIV04/2019进行了比较。基因组比对显示与在南非分离出的奥密克戎变体相似度最高。系统发育分析表明该变体属于21K分支。