Tan, Kim-Kee and Tiong, Vunjia and Tan, Jiun Yan and Wong, Jo-Ern and Teoh, Boon-Teong and Abd-Jamil, Juraina and Johari, Mohd Iskandar Jefree and Nor'e, Siti-Sarah and Khor, Chee Sieng and Yaacob, Che-Norainon and Zulkifli, Mulya-Mustika-Sari and CheMatSeri, AsmaAnati and Mahfodz, Nur-Hidayana and Azizan, Noor Syahida and AbuBakar, Sazaly (2021) Multiplex sequencing of SARS-Cov-2 genome directly from clinical samples using the ion Personal Genome Machine (PGM). Tropical Biomedicine, 38 (3). pp. 283-288. ISSN 2521-9855, DOI https://doi.org/10.47665/tb.38.3.069.
Full text not available from this repository.Abstract
Various methods have been developed for rapid and high throughput full genome sequencing of SARS-CoV-2. Here, we described a protocol for targeted multiplex full genome sequencing of SARS-CoV-2 genomic RNA directly extracted from human nasopharyngeal swabs using the Ion Personal Genome Machine (PGM). This protocol involves concomitant amplification of 237 gene fragments encompassing the SARS-CoV-2 genome to increase the abundance and yield of viral specific sequencing reads. Five complete and one near-complete genome sequences of SARS-CoV-2 were generated with a single Ion PGM sequencing run. The sequence coverage analysis revealed two amplicons (positions 13 751-13 965 and 23 941-24 106), which consistently gave low sequencing read coverage in all isolates except 4Apr20-64-Hu. We analyzed the potential primer binding sites within these low covered regions and noted that the 4Apr20-64-Hu possess C at positions 13 730 and 23 929, whereas the other isolates possess T at these positions. The genome nucleotide variations observed suggest that the naturally occurring variations present in the actively circulating SARS-CoV-2 strains affected the performance of the target enrichment panel of the Ion AmpliSeq (TM) SARS CoV 2 Research Panel. The possible impact of other genome nucleotide variations warrants further investigation, and an improved version of the Ion AmpliSeq (TM) SARS CoV 2 Research Panel, hence, should be considered.
| Item Type: | Article |
|---|---|
| Funders: | Ministry of Energy, Science, Technology, Environment and Climate Change (MESTECC), Malaysia[UM.0000345/KWJ.AK], Ministry of Education, Malaysia, Higher Institution Centre of Excellence (HICoE) program[MO002-2019], University Malaya RU grant[RU002-2019], Fundamental Research Grant Scheme[MRSA/1/2018/SKK08/UM/01/1 (MO012-2017)] |
| Uncontrolled Keywords: | SARS-CoV-2;COVID-19;Infectious diseases;Next generation sequencing;Malaysia |
| Subjects: | Q Science > QR Microbiology R Medicine R Medicine > RB Pathology |
| Divisions: | Deputy Vice Chancellor (Research & Innovation) Office > Tropical Infectious Diseases Research and Education Centre |
| Depositing User: | Ms Zaharah Ramly |
| Date Deposited: | 19 Sep 2022 04:19 |
| Last Modified: | 19 Sep 2022 04:19 |
| URI: | http://eprints.um.edu.my/id/eprint/34664 |
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