On-site sequencing of Sars-Cov-2 genomes identify two variant of concern clusters in Pahang, Malaysia
Timely variant identification is required in respond to effective public health measures. It has been demonstrated that comprehending genetic epidemiology can be aided by a combination of public health expertise and through viral genomic sequencing using Oxford Nanopore Technologies (ONT). The purpo...
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| Format: | Article |
| Language: | English |
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Penerbit Universiti Malaysia Pahang
2023
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| Online Access: | http://umpir.ump.edu.my/id/eprint/38323/1/OnSite%20Sequencing%20Of%20Sars_Cov2%20Genomes%20Identify%20Two%20Variant.pdf |
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| author | Ummu Afeera, Zainulabid Wan Nurliyana, Wan Ramli Raihanah, Haroon Ayesha, Aslam Hussain, Mushtaq Hajar Fauzan, Ahmad |
| author_facet | Ummu Afeera, Zainulabid Wan Nurliyana, Wan Ramli Raihanah, Haroon Ayesha, Aslam Hussain, Mushtaq Hajar Fauzan, Ahmad |
| author_sort | Ummu Afeera, Zainulabid |
| collection | UMP |
| description | Timely variant identification is required in respond to effective public health measures. It has been demonstrated that comprehending genetic epidemiology can be aided by a combination of public health expertise and through viral genomic sequencing using Oxford Nanopore Technologies (ONT). The purpose of this study is to determine the utility of using Oxford Nanopore Sequencing to elucidate the genetic epidemiology in two significant clusters in Pahang, Malaysia. The combined oropharyngeal and nasopharyngeal swabs of clinical specimens from two significant clusters in Pahang, Malaysia, were retrieved for long-read sequencing. Results: We identify Beta and Delta variants as 2 variants of concern from our analysis. We found that the B.1.351 (ß) and B.1.617 (D) variants were responsible for the Taman Tanah Putih Baru and Pasar Kemunting clusters, respectively. In conclusion, ONT long-read sequencing tools offer a practical solution with a number of advantages. ONT devices are compact, affordable, and need little technical hands-on or laboratory equipment to prepare samples. They can also be used to quickly and adaptably execute sequencing analyses and to understand genomic epidemiology. |
| first_indexed | 2024-03-06T13:08:16Z |
| format | Article |
| id | UMPir38323 |
| institution | Universiti Malaysia Pahang |
| language | English |
| last_indexed | 2024-03-06T13:08:16Z |
| publishDate | 2023 |
| publisher | Penerbit Universiti Malaysia Pahang |
| record_format | dspace |
| spelling | UMPir383232023-08-10T04:27:34Z http://umpir.ump.edu.my/id/eprint/38323/ On-site sequencing of Sars-Cov-2 genomes identify two variant of concern clusters in Pahang, Malaysia Ummu Afeera, Zainulabid Wan Nurliyana, Wan Ramli Raihanah, Haroon Ayesha, Aslam Hussain, Mushtaq Hajar Fauzan, Ahmad Q Science (General) RA Public aspects of medicine Timely variant identification is required in respond to effective public health measures. It has been demonstrated that comprehending genetic epidemiology can be aided by a combination of public health expertise and through viral genomic sequencing using Oxford Nanopore Technologies (ONT). The purpose of this study is to determine the utility of using Oxford Nanopore Sequencing to elucidate the genetic epidemiology in two significant clusters in Pahang, Malaysia. The combined oropharyngeal and nasopharyngeal swabs of clinical specimens from two significant clusters in Pahang, Malaysia, were retrieved for long-read sequencing. Results: We identify Beta and Delta variants as 2 variants of concern from our analysis. We found that the B.1.351 (ß) and B.1.617 (D) variants were responsible for the Taman Tanah Putih Baru and Pasar Kemunting clusters, respectively. In conclusion, ONT long-read sequencing tools offer a practical solution with a number of advantages. ONT devices are compact, affordable, and need little technical hands-on or laboratory equipment to prepare samples. They can also be used to quickly and adaptably execute sequencing analyses and to understand genomic epidemiology. Penerbit Universiti Malaysia Pahang 2023-06 Article PeerReviewed pdf en cc_by_4 http://umpir.ump.edu.my/id/eprint/38323/1/OnSite%20Sequencing%20Of%20Sars_Cov2%20Genomes%20Identify%20Two%20Variant.pdf Ummu Afeera, Zainulabid and Wan Nurliyana, Wan Ramli and Raihanah, Haroon and Ayesha, Aslam and Hussain, Mushtaq and Hajar Fauzan, Ahmad (2023) On-site sequencing of Sars-Cov-2 genomes identify two variant of concern clusters in Pahang, Malaysia. Current Science and Technology (CST), 2 (2). pp. 1-7. ISSN 2785-8804. (Published) https://doi.org/10.15282/cst.v2i2.8859 https://doi.org/10.15282/cst.v2i2.8859 |
| spellingShingle | Q Science (General) RA Public aspects of medicine Ummu Afeera, Zainulabid Wan Nurliyana, Wan Ramli Raihanah, Haroon Ayesha, Aslam Hussain, Mushtaq Hajar Fauzan, Ahmad On-site sequencing of Sars-Cov-2 genomes identify two variant of concern clusters in Pahang, Malaysia |
| title | On-site sequencing of Sars-Cov-2 genomes identify two variant of concern clusters in Pahang, Malaysia |
| title_full | On-site sequencing of Sars-Cov-2 genomes identify two variant of concern clusters in Pahang, Malaysia |
| title_fullStr | On-site sequencing of Sars-Cov-2 genomes identify two variant of concern clusters in Pahang, Malaysia |
| title_full_unstemmed | On-site sequencing of Sars-Cov-2 genomes identify two variant of concern clusters in Pahang, Malaysia |
| title_short | On-site sequencing of Sars-Cov-2 genomes identify two variant of concern clusters in Pahang, Malaysia |
| title_sort | on site sequencing of sars cov 2 genomes identify two variant of concern clusters in pahang malaysia |
| topic | Q Science (General) RA Public aspects of medicine |
| url | http://umpir.ump.edu.my/id/eprint/38323/1/OnSite%20Sequencing%20Of%20Sars_Cov2%20Genomes%20Identify%20Two%20Variant.pdf |
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