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Lebanese SARS-CoV-2 genomics: 24 months of the pandemic
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 s...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier B.V.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9121641/ https://www.ncbi.nlm.nih.gov/pubmed/35605880 http://dx.doi.org/10.1016/j.virusres.2022.198824 |
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author | Fayad, Nancy Habib, Walid Abi El-Shesheny, Rabeh Kandeil, Ahmed Mourad, Youmna Mokhbat, Jacques Kayali, Ghazi Goldstein, Jimi Abdallah, Jad |
author_facet | Fayad, Nancy Habib, Walid Abi El-Shesheny, Rabeh Kandeil, Ahmed Mourad, Youmna Mokhbat, Jacques Kayali, Ghazi Goldstein, Jimi Abdallah, Jad |
author_sort | Fayad, Nancy |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-9121641 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Elsevier B.V. |
record_format | MEDLINE/PubMed |
spelling | pubmed-91216412022-05-20 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 Virus Res Article 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. Elsevier B.V. 2022-08 2022-05-20 /pmc/articles/PMC9121641/ /pubmed/35605880 http://dx.doi.org/10.1016/j.virusres.2022.198824 Text en © 2022 Elsevier B.V. All rights reserved. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. |
spellingShingle | Article Fayad, Nancy Habib, Walid Abi El-Shesheny, Rabeh Kandeil, Ahmed Mourad, Youmna Mokhbat, Jacques Kayali, Ghazi Goldstein, Jimi Abdallah, Jad Lebanese SARS-CoV-2 genomics: 24 months of the pandemic |
title | Lebanese SARS-CoV-2 genomics: 24 months of the pandemic |
title_full | Lebanese SARS-CoV-2 genomics: 24 months of the pandemic |
title_fullStr | Lebanese SARS-CoV-2 genomics: 24 months of the pandemic |
title_full_unstemmed | Lebanese SARS-CoV-2 genomics: 24 months of the pandemic |
title_short | Lebanese SARS-CoV-2 genomics: 24 months of the pandemic |
title_sort | lebanese sars-cov-2 genomics: 24 months of the pandemic |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9121641/ https://www.ncbi.nlm.nih.gov/pubmed/35605880 http://dx.doi.org/10.1016/j.virusres.2022.198824 |
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