Characterization of the SARS-CoV-2 genomes in Egypt in first and second waves of infection

Abstract

At Wuhan, in December 2019, the SRAS-CoV-2 outbreak was detected and it has been the pandemic worldwide. This study aims to investigate the mutations in sequence of the SARS-CoV-2 genome and characterize the mutation patterns in Egyptian COVID-19 patients during different waves of infection. The samples were collected from 250 COVID-19 patients and the whole genome sequencing was conducted using Next Generation Sequencing. The viral sequence analysis showed 1115 different genome from all Egyptian samples in the second wave mutations including 613 missense mutations, 431 synonymous mutations, 25 upstream gene mutations, 24 downstream gene mutations, 10 frame-shift deletions, and 6 stop gained mutation. The Egyptian genomic strains sequenced in second wave of infection are different to that of the first wave. We observe a shift of lineage prevalence from the strain B.1 to B.1.1.1. Only one case was of the new English B.1.1.7. Few samples have one or two mutations of interest from the Brazil and South Africa isolates. New clade 20B appear by March 2020 and 20D appear by May 2020 till January 2021.

Whole-genome sequencing of SARS-CoV-2 reveals diverse mutations in circulating Alpha and Delta variants during the first, second, and third waves of COVID-19 in South Kivu, east of the Democratic Republic of the Congo

“…Our study shows a higher number of missense mutations than synonymous mutations, and half of them were located in the ORF1ab gene followed by the S gene (49 missense mutations). A similar observation was reported in studies conducted in Colombia and Egypt ( Bermúdez-Forero et al, 2021 ;Sahin et al, 2021 ;Zekri et al, 2021 ;Maitra et al, 2020 ). Interestingly, the L4715L mutation found in 60 SARS-CoV-2 sequences from this study corroborates with previous findings reporting the P4715L mutation as a potential antiviral drug target ( Pachetti et al, 2020 ).…”

SARS-CoV-2 genome variations and evolution patterns in Egypt: a multi-center study

“…S477N and P681H were found to confer resistance to antibody therapy 29 , 33 , whereas contradictory reports were reported for IHV68I 34 , 35 . A study on 176 viral genome sequences from Egypt showed mutation patterns similar to those found in our data 36 .…”

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

“…Towards the end of 2020, more distinct viral lineages started to appear. The most important of which that impacted the African continent are: B.1.525 (n=797), B.1.1.318 (n=398) ( 35 ), B.1.1.418 (n=395), A.23.1 (n=358) (( 15, 29, 31, 33 )), C.1 (n=446) ( 29 ), C.1.2 (n=300) ( 31 ), C.36 (n=305) ( 30, 36 ), B.1.1.54 (n=287) (( 15, 29, 31, 33 )), B.1.416 (n=272), B.1.177 (n=203), B.1.620 (n=138), and B.1.160 (n=61), ( 32 ) ( Supp Fig S3A,B ). From our discrete state phylogeographic inference we infer at least 2,151 (95% CI: 2,132 - 2,170) viral introductions of non-VOC lineages into African countries over the course of the pandemic.…”