Whole genome sequencing analysis of SARS-CoV-2 from Malaysia: from alpha to Omicron
Countries around the world are gearing for the transition of the coronavirus disease 2019 (COVID-19) from pandemic to endemic phase but the emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants could lead to a prolonged pandemic. SARS-CoV-2 has continued to evolve as...
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Frontiers Research Foundation
2022
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| author | Choo, Yee Yu Sie, Yeng Wong Woan, Nancy Charn Liew Joseph, Narcisse Zakaria, Zunita Isa, Nurulfiza Hui, Jen Soe Kairon, Rachna Amin Nordin, Syafinaz Hui, Yee Chee |
| author_facet | Choo, Yee Yu Sie, Yeng Wong Woan, Nancy Charn Liew Joseph, Narcisse Zakaria, Zunita Isa, Nurulfiza Hui, Jen Soe Kairon, Rachna Amin Nordin, Syafinaz Hui, Yee Chee |
| author_sort | Choo, Yee Yu |
| collection | UPM |
| description | Countries around the world are gearing for the transition of the coronavirus disease 2019 (COVID-19) from pandemic to endemic phase but the emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants could lead to a prolonged pandemic. SARS-CoV-2 has continued to evolve as it optimizes its adaptation to the human host and the successive waves of COVID-19 have been linked to the explosion of particular variant of concern. As the genetic diversity and epidemiological landscape of SARS-CoV-2 differ from country to country, this study aims to provide insights into the variants that are circulating in Malaysia. Whole genome sequencing was performed for 204 SARS-CoV-2 from COVID-19 cases and an additional 18,667 SARS-CoV-2 genome sequences were retrieved from the GISAID EpiCoV database for clade, lineage and genetic variation analyses. Complete genome sequences with high coverage were then used for phylogeny investigation and the resulting phylogenetic tree was constructed from 8,716 sequences. We found that the different waves of COVID-19 in Malaysia were dominated by different clades with the L and O clade for first and second wave, respectively, whereas the progressive replacement by G, GH, and GK of the GRA clade were observed in the subsequence waves. Continuous monitoring of the genetic diversity of SARS-CoV-2 is important to identify the emergence and dominance of new variant in different locality so that the appropriate countermeasures can be taken to effectively contain the spread of SARS-CoV-2. |
| first_indexed | 2024-03-06T11:17:45Z |
| format | Article |
| id | upm.eprints-102636 |
| institution | Universiti Putra Malaysia |
| last_indexed | 2024-03-06T11:17:45Z |
| publishDate | 2022 |
| publisher | Frontiers Research Foundation |
| record_format | dspace |
| spelling | upm.eprints-1026362023-10-16T02:37:39Z http://psasir.upm.edu.my/id/eprint/102636/ Whole genome sequencing analysis of SARS-CoV-2 from Malaysia: from alpha to Omicron Choo, Yee Yu Sie, Yeng Wong Woan, Nancy Charn Liew Joseph, Narcisse Zakaria, Zunita Isa, Nurulfiza Hui, Jen Soe Kairon, Rachna Amin Nordin, Syafinaz Hui, Yee Chee Countries around the world are gearing for the transition of the coronavirus disease 2019 (COVID-19) from pandemic to endemic phase but the emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants could lead to a prolonged pandemic. SARS-CoV-2 has continued to evolve as it optimizes its adaptation to the human host and the successive waves of COVID-19 have been linked to the explosion of particular variant of concern. As the genetic diversity and epidemiological landscape of SARS-CoV-2 differ from country to country, this study aims to provide insights into the variants that are circulating in Malaysia. Whole genome sequencing was performed for 204 SARS-CoV-2 from COVID-19 cases and an additional 18,667 SARS-CoV-2 genome sequences were retrieved from the GISAID EpiCoV database for clade, lineage and genetic variation analyses. Complete genome sequences with high coverage were then used for phylogeny investigation and the resulting phylogenetic tree was constructed from 8,716 sequences. We found that the different waves of COVID-19 in Malaysia were dominated by different clades with the L and O clade for first and second wave, respectively, whereas the progressive replacement by G, GH, and GK of the GRA clade were observed in the subsequence waves. Continuous monitoring of the genetic diversity of SARS-CoV-2 is important to identify the emergence and dominance of new variant in different locality so that the appropriate countermeasures can be taken to effectively contain the spread of SARS-CoV-2. Frontiers Research Foundation 2022-09-23 Article PeerReviewed Choo, Yee Yu and Sie, Yeng Wong and Woan, Nancy Charn Liew and Joseph, Narcisse and Zakaria, Zunita and Isa, Nurulfiza and Hui, Jen Soe and Kairon, Rachna and Amin Nordin, Syafinaz and Hui, Yee Chee (2022) Whole genome sequencing analysis of SARS-CoV-2 from Malaysia: from alpha to Omicron. Frontiers, 9. Jan-13. ISSN 2296-858X https://www.frontiersin.org/research-topics/34105/emerging-sars-cov-2-variants-genomic-variations-transmission-pathogenesis-clinical-impact-and-interventions-volume-ii#articles 10.3389/fmed.2022.1001022 |
| spellingShingle | Choo, Yee Yu Sie, Yeng Wong Woan, Nancy Charn Liew Joseph, Narcisse Zakaria, Zunita Isa, Nurulfiza Hui, Jen Soe Kairon, Rachna Amin Nordin, Syafinaz Hui, Yee Chee Whole genome sequencing analysis of SARS-CoV-2 from Malaysia: from alpha to Omicron |
| title | Whole genome sequencing analysis of SARS-CoV-2 from Malaysia: from alpha to Omicron |
| title_full | Whole genome sequencing analysis of SARS-CoV-2 from Malaysia: from alpha to Omicron |
| title_fullStr | Whole genome sequencing analysis of SARS-CoV-2 from Malaysia: from alpha to Omicron |
| title_full_unstemmed | Whole genome sequencing analysis of SARS-CoV-2 from Malaysia: from alpha to Omicron |
| title_short | Whole genome sequencing analysis of SARS-CoV-2 from Malaysia: from alpha to Omicron |
| title_sort | whole genome sequencing analysis of sars cov 2 from malaysia from alpha to omicron |
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