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A multi-population-based genomic analysis uncovers unique haplotype variants and crucial mutant genes in SARS-CoV-2
BACKGROUND: COVID-19 is a disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Rigorous detection and treatment strategies against SARS-CoV-2 have become very challenging due to continuous evolutions to the viral genome. Therefore, careful genomic analysis is sorely needed...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer Berlin Heidelberg
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9626712/ https://www.ncbi.nlm.nih.gov/pubmed/36318347 http://dx.doi.org/10.1186/s43141-022-00431-3 |
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author | Sheikh, Afzal Huang, He Parvin, Sultana Badruzzaman, Mohammad Ahamed, Tofayel Hossain, Ekhtear Baran, Iri Sato Saud, Zahangir Alam |
author_facet | Sheikh, Afzal Huang, He Parvin, Sultana Badruzzaman, Mohammad Ahamed, Tofayel Hossain, Ekhtear Baran, Iri Sato Saud, Zahangir Alam |
author_sort | Sheikh, Afzal |
collection | PubMed |
description | BACKGROUND: COVID-19 is a disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Rigorous detection and treatment strategies against SARS-CoV-2 have become very challenging due to continuous evolutions to the viral genome. Therefore, careful genomic analysis is sorely needed to understand transmission, the cellular mechanism of pathogenicity, and the development of vaccines or drugs. OBJECTIVE: In this study, we intended to identify SARS-CoV-2 genome variants that may help understand the cellular and molecular foundation of coronavirus infections required to develop effective intervention strategies. METHODS: SARS-CoV-2 genome sequences were downloaded from an open-source public database, processed, and analyzed for variants in target detection sites and genes. RESULTS: We have identified six unique variants, G---AAC, T---AAC---T, AAC---T, AAC--------T, C----------T, and C--------C, at the nucleocapsid region and eleven major hotspot mutant genes: nsp3, surface glycoprotein, nucleocapsid phosphoprotein, ORF8, nsp6, nsp2, nsp4, helicase, membrane glycoprotein, 3′-5′ exonuclease, and 2′-O-ribose methyltransferases. In addition, we have identified eleven major mutant genes that may have a crucial role in SARS-CoV-2 pathogenesis. CONCLUSION: Studying haplotype variants and 11 major mutant genes to understand the mechanism of action of fatal pathogenicity and inter-individual variations in immune responses is inevitable for managing target patient groups with identified variants and developing effective anti-viral drugs and vaccines. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s43141-022-00431-3. |
format | Online Article Text |
id | pubmed-9626712 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Springer Berlin Heidelberg |
record_format | MEDLINE/PubMed |
spelling | pubmed-96267122022-11-02 A multi-population-based genomic analysis uncovers unique haplotype variants and crucial mutant genes in SARS-CoV-2 Sheikh, Afzal Huang, He Parvin, Sultana Badruzzaman, Mohammad Ahamed, Tofayel Hossain, Ekhtear Baran, Iri Sato Saud, Zahangir Alam J Genet Eng Biotechnol Research BACKGROUND: COVID-19 is a disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Rigorous detection and treatment strategies against SARS-CoV-2 have become very challenging due to continuous evolutions to the viral genome. Therefore, careful genomic analysis is sorely needed to understand transmission, the cellular mechanism of pathogenicity, and the development of vaccines or drugs. OBJECTIVE: In this study, we intended to identify SARS-CoV-2 genome variants that may help understand the cellular and molecular foundation of coronavirus infections required to develop effective intervention strategies. METHODS: SARS-CoV-2 genome sequences were downloaded from an open-source public database, processed, and analyzed for variants in target detection sites and genes. RESULTS: We have identified six unique variants, G---AAC, T---AAC---T, AAC---T, AAC--------T, C----------T, and C--------C, at the nucleocapsid region and eleven major hotspot mutant genes: nsp3, surface glycoprotein, nucleocapsid phosphoprotein, ORF8, nsp6, nsp2, nsp4, helicase, membrane glycoprotein, 3′-5′ exonuclease, and 2′-O-ribose methyltransferases. In addition, we have identified eleven major mutant genes that may have a crucial role in SARS-CoV-2 pathogenesis. CONCLUSION: Studying haplotype variants and 11 major mutant genes to understand the mechanism of action of fatal pathogenicity and inter-individual variations in immune responses is inevitable for managing target patient groups with identified variants and developing effective anti-viral drugs and vaccines. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s43141-022-00431-3. Springer Berlin Heidelberg 2022-11-01 /pmc/articles/PMC9626712/ /pubmed/36318347 http://dx.doi.org/10.1186/s43141-022-00431-3 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Research Sheikh, Afzal Huang, He Parvin, Sultana Badruzzaman, Mohammad Ahamed, Tofayel Hossain, Ekhtear Baran, Iri Sato Saud, Zahangir Alam A multi-population-based genomic analysis uncovers unique haplotype variants and crucial mutant genes in SARS-CoV-2 |
title | A multi-population-based genomic analysis uncovers unique haplotype variants and crucial mutant genes in SARS-CoV-2 |
title_full | A multi-population-based genomic analysis uncovers unique haplotype variants and crucial mutant genes in SARS-CoV-2 |
title_fullStr | A multi-population-based genomic analysis uncovers unique haplotype variants and crucial mutant genes in SARS-CoV-2 |
title_full_unstemmed | A multi-population-based genomic analysis uncovers unique haplotype variants and crucial mutant genes in SARS-CoV-2 |
title_short | A multi-population-based genomic analysis uncovers unique haplotype variants and crucial mutant genes in SARS-CoV-2 |
title_sort | multi-population-based genomic analysis uncovers unique haplotype variants and crucial mutant genes in sars-cov-2 |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9626712/ https://www.ncbi.nlm.nih.gov/pubmed/36318347 http://dx.doi.org/10.1186/s43141-022-00431-3 |
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