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Tan KK, Tiong V, Tan JY, Wong JE, Teoh BT, Abd-Jamil J, Johari J, Nor'e SS, Khor CS, Yaacob CN, Zulkifli MMS, CheMatSeri A, Mahfodz NH, Azizan NS, AbuBakar S. Multiplex sequencing of SARS-Cov-2 genome directly from clinical samples using the Ion Personal Genome Machine (PGM). Trop Biomed 2021; 38:283-288. [PMID: 34362871 DOI: 10.47665/tb.38.3.069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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™ SARS CoV 2 Research Panel. The possible impact of other genome nucleotide variations warrants further investigation, and an improved version of the Ion AmpliSeq™ SARS CoV 2 Research Panel, hence, should be considered.
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Affiliation(s)
- K K Tan
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - V Tiong
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - J Y Tan
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - J E Wong
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - B T Teoh
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - J Abd-Jamil
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - J Johari
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - S S Nor'e
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - C S Khor
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - C N Yaacob
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - M M S Zulkifli
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - A CheMatSeri
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - N H Mahfodz
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - N S Azizan
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - S AbuBakar
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), University of Malaya, 50603 Kuala Lumpur, Malaysia.,Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
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