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Lebanese SARS-CoV-2 genomics: 24 months of the pandemic.
Fayad, Nancy; Habib, Walid Abi; El-Shesheny, Rabeh; Kandeil, Ahmed; Mourad, Youmna; Mokhbat, Jacques; Kayali, Ghazi; Goldstein, Jimi; Abdallah, Jad.
  • Fayad N; Multi-Omics Laboratory, School of Pharmacy, Lebanese American University, P.O. Box 36, Byblos 1401, Lebanon.
  • Habib WA; Multi-Omics Laboratory, School of Pharmacy, Lebanese American University, P.O. Box 36, Byblos 1401, Lebanon.
  • El-Shesheny R; Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt.
  • Kandeil A; Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, United States of America.
  • Mourad Y; Al Hadi Laboratory and IVF Center, Beirut, Lebanon.
  • Mokhbat J; School of Medicine, Lebanese American University, P.O. Box 36, Byblos, Lebanon.
  • Kayali G; Human Link, Dubai, United Arab Emirates.
  • Goldstein J; Human Link, Dubai, United Arab Emirates; School of Engineering and Technology, University of Hertfordshire, Hatfield, Hertfordshire AL10 9AB, UK. Electronic address: jimi@human-link.org.
  • Abdallah J; Multi-Omics Laboratory, School of Pharmacy, Lebanese American University, P.O. Box 36, Byblos 1401, Lebanon. Electronic address: jabdallah@lau.edu.lb.
Virus Res ; 317: 198824, 2022 08.
Article in English | MEDLINE | ID: covidwho-1852224
ABSTRACT
The COVID-19 pandemic continues to pose a global health concern, despite the ongoing vaccination campaigns, due to the emergence and rapid spread of new variants of the causative agent SARS-CoV-2. These variants are identified and tracked via the marker mutations they carry, and the classification system put in place following tremendous sequencing efforts. In this study, the genomes of 1,230 Lebanese SARS-CoV-2 strains collected throughout 2 years of the outbreak in Lebanon were analyzed, 115 of which sequenced within this project. Strains were classified into seven GISAID clades, the major one being GRY, and 36 Pango lineages, with three variants of concern identified alpha, delta and omicron. A time course distribution of GISAID clades allowed the visualization of change throughout the two years of the Lebanese outbreak, in conjunction with major events and measures in the country. Subsequent phylogenetic analysis showed the clustering of strains belonging to the same clades. In addition, a mutational survey showed the presence of mutations in the structural, non-structural and accessory proteins. Twenty five (25) mutations were labeled as major, i.e. present in more than 30% of the strains, such as the common Spike_D614G and NSP3_T183I. Whereas 635 were labeled as uncommon, i.e. found in very few of the analyzed strains as well as GISAID records, such as NSP2_I349V. Distribution of these mutations differed between 2020, and the first and the second half of 2021. In summary, this study highlights key genomic aspects of the Lebanese SARS-CoV-2 strains collected in 2020, the first year of the outbreak in Lebanon, versus those collected in 2021, the second year of COVID-19 in Lebanon.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study / Randomized controlled trials Topics: Vaccines / Variants Limits: Humans Language: English Journal: Virus Res Journal subject: Virology Year: 2022 Document Type: Article Affiliation country: J.virusres.2022.198824

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study / Randomized controlled trials Topics: Vaccines / Variants Limits: Humans Language: English Journal: Virus Res Journal subject: Virology Year: 2022 Document Type: Article Affiliation country: J.virusres.2022.198824