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. 2022 Jul 7:13:923137.
doi: 10.3389/fmicb.2022.923137. eCollection 2022.

The Mutational Landscape of SARS-CoV-2 Variants of Concern Recovered From Egyptian Patients in 2021

Mohamed G Seadawy  1 , Reem Binsuwaidan  2 , Badriyah Alotaibi  2 , Thanaa A El-Masry  3 , Bassem E El-Harty  1 , Ahmed F Gad  1 , Walid F Elkhatib  4   5 , Maisra M El-Bouseary  6
Affiliations

The Mutational Landscape of SARS-CoV-2 Variants of Concern Recovered From Egyptian Patients in 2021

Mohamed G Seadawy et al. Front Microbiol. .

Abstract

In December 2019, a mysterious viral pneumonia first developed in Wuhan, China, resulting in a huge number of fatal cases. This pneumonia, which was named COVID-19, was attributed to a novel coronavirus, SARS-CoV-2. The emerging SARS-CoV-2 mutations pose the greatest risk to human health because they could result in an increase in the COVID-19 severity or the failure of current vaccines. One of these notable mutations is the SARS-CoV-2 Delta variant (B.1.617) that was first detected in India and has rapidly expanded to 115 countries worldwide. Consequently, in this study, we performed next-generation sequencing and phylogenetic analysis of SARS-CoV-2 during the third wave of the pandemic to determine the SARS-CoV-2 variants of concern (VOC) prevalence in Egypt. We observed several mutational patterns, revealing that SARS-CoV-2 evolution has expanded in Egypt with a considerable increase in the number of VOC. Therefore, the Egyptian authorities should take an appropriate approach to investigate the compatibility of already employed vaccines with this VOC and to examine the efficacy of the existing therapeutic regimen against new SARS-CoV-2 variants.

Keywords: Egypt; SARS-CoV-2; alpha variant; delta variant; next generation sequencing; phylogenetic analysis; variant of concern.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Bar chart showing both the number of patients exhibiting COVID-19 symptoms.
Figure 2
Figure 2
Rectangular phylogenetic tree showing the distribution of sequences among different clades (https://clades.nextstrain.org/tree).
Figure 3
Figure 3
The divergence of tested SARS-CoV-2 genomes in comparison to the reference strain Wuhan-Hu-1.
Figure 4
Figure 4
The frequency of mutations observed among different genes. (A) ORF1a; (B) ORF1b; (C) S; (D) ORF3a; (E) M, ORF7, ORF8 and ORF9; (F) N; (G) number of mutational sites distributed among genes.
Figure 5
Figure 5
Spike glycoprotein associated with the host cell receptor ACE2 (green ribbon). (A) 20I (Alpha variant); (B) 21A (Delta variant); (C) 21I (Delta variant); (D) 21 J (Delta variant); and (E) overall changes in all sequences tested. Colored balls present amino acid variations: A222V, A570D, A871S, D138Y, D178H, D178Y, D614G, D950N, E156G, E484K, G181V, H655Y, Q173H, Q613H, Q677H, S982A, T95I, T572I, T716I, W64R in blue. A899S, D1118H, E484Q, L452R, N501T, N501Y, P681H, P681R, R346S, T478K, W152R in orange. A292V, G1124R in gray. F157del, R158del in turquoise. T19R in fuchsia.
Figure 6
Figure 6
Molecular phylogenetic analysis by the Maximum Likelihood method.
See this image and copyright information in PMC

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