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Characterization of the SARS-CoV-2 genomes in Egypt in first and second waves of infection.
Zekri, Abdel-Rahman N; Bahnasy, Abeer A; Hafez, Mohamed M; Hassan, Zeinab K; Ahmed, Ola S; Soliman, Hany K; El-Sisi, Enas R; Dine, Mona H Salah El; Solimane, May S; Latife, Lamyaa S Abdel; Seadawy, Mohamed G; Elsafty, Ahmed S; Abouelhoda, Mohamed.
  • Zekri AN; Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, 11796, Egypt. Abdelrhman.zekri@nci.cu.edu.eg.
  • Bahnasy AA; Surgical Pathology Department, National Cancer Institute, Cairo University, Cairo, 11796, Egypt.
  • Hafez MM; Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, 11796, Egypt.
  • Hassan ZK; Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, 11796, Egypt.
  • Ahmed OS; Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, 11796, Egypt.
  • Soliman HK; Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, 11796, Egypt.
  • El-Sisi ER; Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, 11796, Egypt.
  • Dine MHSE; Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt.
  • Solimane MS; Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt.
  • Latife LSA; Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt.
  • Seadawy MG; Main Chemical Laboratories, Egypt Army, Cairo, Egypt.
  • Elsafty AS; Main Chemical Laboratories, Egypt Army, Cairo, Egypt.
  • Abouelhoda M; Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo, 12613, Egypt.
Sci Rep ; 11(1): 21632, 2021 11 03.
Article in English | MEDLINE | ID: covidwho-1500753
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Genome, Viral / Whole Genome Sequencing / SARS-CoV-2 Type of study: Observational study / Randomized controlled trials Limits: Humans Language: English Journal: Sci Rep Year: 2021 Document Type: Article Affiliation country: S41598-021-99014-4

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Genome, Viral / Whole Genome Sequencing / SARS-CoV-2 Type of study: Observational study / Randomized controlled trials Limits: Humans Language: English Journal: Sci Rep Year: 2021 Document Type: Article Affiliation country: S41598-021-99014-4