Alternative genome sequencing approaches of SARS-CoV-2 using Ion AmpliSeq Technology
A thorough understanding of SARS-CoV-2 genetic features is compulsory to track the ongoing pandemic across multiple geographical locations of the world. Thermo Fisher Scientific USA has developed the Ion AmpliSeq SARS-CoV-2 Research Panel for the targeted sequencing of SARS-CoV-2 complete genome wit...
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| Format: | Article |
| Language: | English |
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Elsevier
2024-06-01
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| Series: | MethodsX |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2215016124001006 |
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| author | Md. Shazid Hasan M. Shaminur Rahman Prosanto Kumar Das A.S.M. Rubayet Ul Alam Ovinu Kibria Islam Hassan M. Al-Emran M. Anwar Hossain Iqbal Kabir Jahid |
| author_facet | Md. Shazid Hasan M. Shaminur Rahman Prosanto Kumar Das A.S.M. Rubayet Ul Alam Ovinu Kibria Islam Hassan M. Al-Emran M. Anwar Hossain Iqbal Kabir Jahid |
| author_sort | Md. Shazid Hasan |
| collection | DOAJ |
| description | A thorough understanding of SARS-CoV-2 genetic features is compulsory to track the ongoing pandemic across multiple geographical locations of the world. Thermo Fisher Scientific USA has developed the Ion AmpliSeq SARS-CoV-2 Research Panel for the targeted sequencing of SARS-CoV-2 complete genome with high coverage and lower error rate. In this study an alternative approach of complete genome sequencing has been validated using different commercial sequencing kits to sequence the SARS-CoV-2. Amplification of cDNA with the SARS-CoV-2 primer pool was performed separately using two different master mixes: 2X environmental master mix (EM) and Platinum™ PCR SuperMix High Fidelity master mix (PM) instead of 5X Ion AmpliSeq™ HiFi Mix whereas NEBNext® Fast DNA Library Prep Set for Ion Torrent™ kit was used as an alternative to Ion AmpliSeq Library Kit Plus for other reagents. This study demonstrated a successful procedure to sequence the SARS-CoV-2 whole genome with average ∼2351 depth and 98.1% of total the reads aligned against the reference sequence (SARS-CoV-2, isolate Wuhan-Hu-1, complete genome). Although genome coverage varied, complete genomes were retrieved for both reagent sets with a reduced cost. This study proposed an alternative approach of high throughput sequencing using Ion torrent technology for the sequencing of SARS-CoV-2 in developing countries where sequencing facilities are low. This blended sequencing technique also offers a low cost protocol in developing countries like Bangladesh. |
| first_indexed | 2024-04-24T23:17:54Z |
| format | Article |
| id | doaj.art-e91e15c0395b48ab8c195281108d095c |
| institution | Directory Open Access Journal |
| issn | 2215-0161 |
| language | English |
| last_indexed | 2024-04-24T23:17:54Z |
| publishDate | 2024-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | MethodsX |
| spelling | doaj.art-e91e15c0395b48ab8c195281108d095c2024-03-17T07:54:26ZengElsevierMethodsX2215-01612024-06-0112102646Alternative genome sequencing approaches of SARS-CoV-2 using Ion AmpliSeq TechnologyMd. Shazid Hasan0M. Shaminur Rahman1Prosanto Kumar Das2A.S.M. Rubayet Ul Alam3Ovinu Kibria Islam4Hassan M. Al-Emran5M. Anwar Hossain6Iqbal Kabir Jahid7Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, BangladeshDepartment of Microbiology, Jashore University of Science and Technology, Jashore 7408, BangladeshDepartment of Microbiology, Jashore University of Science and Technology, Jashore 7408, BangladeshDepartment of Microbiology, Jashore University of Science and Technology, Jashore 7408, BangladeshDepartment of Microbiology, Jashore University of Science and Technology, Jashore 7408, BangladeshDepartment of Biomedical Engineering, Jashore University of Science and Technology, Jashore 7408, BangladeshGenome Centre, Jashore University of Science and Technology, Jashore 7408, BangladeshDepartment of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Corresponding author at: Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh.A thorough understanding of SARS-CoV-2 genetic features is compulsory to track the ongoing pandemic across multiple geographical locations of the world. Thermo Fisher Scientific USA has developed the Ion AmpliSeq SARS-CoV-2 Research Panel for the targeted sequencing of SARS-CoV-2 complete genome with high coverage and lower error rate. In this study an alternative approach of complete genome sequencing has been validated using different commercial sequencing kits to sequence the SARS-CoV-2. Amplification of cDNA with the SARS-CoV-2 primer pool was performed separately using two different master mixes: 2X environmental master mix (EM) and Platinum™ PCR SuperMix High Fidelity master mix (PM) instead of 5X Ion AmpliSeq™ HiFi Mix whereas NEBNext® Fast DNA Library Prep Set for Ion Torrent™ kit was used as an alternative to Ion AmpliSeq Library Kit Plus for other reagents. This study demonstrated a successful procedure to sequence the SARS-CoV-2 whole genome with average ∼2351 depth and 98.1% of total the reads aligned against the reference sequence (SARS-CoV-2, isolate Wuhan-Hu-1, complete genome). Although genome coverage varied, complete genomes were retrieved for both reagent sets with a reduced cost. This study proposed an alternative approach of high throughput sequencing using Ion torrent technology for the sequencing of SARS-CoV-2 in developing countries where sequencing facilities are low. This blended sequencing technique also offers a low cost protocol in developing countries like Bangladesh.http://www.sciencedirect.com/science/article/pii/S2215016124001006Alternative approaches of SARS-CoV-2 complete genome sequencing |
| spellingShingle | Md. Shazid Hasan M. Shaminur Rahman Prosanto Kumar Das A.S.M. Rubayet Ul Alam Ovinu Kibria Islam Hassan M. Al-Emran M. Anwar Hossain Iqbal Kabir Jahid Alternative genome sequencing approaches of SARS-CoV-2 using Ion AmpliSeq Technology MethodsX Alternative approaches of SARS-CoV-2 complete genome sequencing |
| title | Alternative genome sequencing approaches of SARS-CoV-2 using Ion AmpliSeq Technology |
| title_full | Alternative genome sequencing approaches of SARS-CoV-2 using Ion AmpliSeq Technology |
| title_fullStr | Alternative genome sequencing approaches of SARS-CoV-2 using Ion AmpliSeq Technology |
| title_full_unstemmed | Alternative genome sequencing approaches of SARS-CoV-2 using Ion AmpliSeq Technology |
| title_short | Alternative genome sequencing approaches of SARS-CoV-2 using Ion AmpliSeq Technology |
| title_sort | alternative genome sequencing approaches of sars cov 2 using ion ampliseq technology |
| topic | Alternative approaches of SARS-CoV-2 complete genome sequencing |
| url | http://www.sciencedirect.com/science/article/pii/S2215016124001006 |
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