Alternative genome sequencing approaches of SARS-CoV-2 using Ion AmpliSeq Technology.

Autor:	Hasan MS; Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh., Rahman MS; Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh., Das PK; Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh., Ul Alam ASMR; Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh., Islam OK; Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh., Al-Emran HM; Department of Biomedical Engineering, Jashore University of Science and Technology, Jashore 7408, Bangladesh., Hossain MA; Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh., Jahid IK; Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh.; Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh.
Jazyk:	angličtina
Zdroj:	MethodsX [MethodsX] 2024 Mar 11; Vol. 12, pp. 102646. Date of Electronic Publication: 2024 Mar 11 (Print Publication: 2024).
DOI:	10.1016/j.mex.2024.102646
Abstrakt:	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. Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. (© 2024 The Authors. Published by Elsevier B.V.)
Databáze:	MEDLINE
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