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Universal whole-genome Oxford nanopore sequencing of SARS-CoV-2 using tiled amplicons
We developed a comprehensive multiplexed set of primers adapted for the Oxford Nanopore Rapid Barcoding library kit that allows universal SARS-CoV-2 genome sequencing. This primer set is designed to set up any variants of the primers pool for whole-genome sequencing of SARS-CoV-2 using single- or do...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10293217/ https://www.ncbi.nlm.nih.gov/pubmed/37365249 http://dx.doi.org/10.1038/s41598-023-37588-x |
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author | Kalendar, Ruslan Kairov, Ulykbek Karabayev, Daniyar Aitkulova, Akbota Tynyshtykbayeva, Nuray Daniyarov, Asset Otarbay, Zhenis Rakhimova, Saule Akilzhanova, Ainur Sarbassov, Dos |
author_facet | Kalendar, Ruslan Kairov, Ulykbek Karabayev, Daniyar Aitkulova, Akbota Tynyshtykbayeva, Nuray Daniyarov, Asset Otarbay, Zhenis Rakhimova, Saule Akilzhanova, Ainur Sarbassov, Dos |
author_sort | Kalendar, Ruslan |
collection | PubMed |
description | We developed a comprehensive multiplexed set of primers adapted for the Oxford Nanopore Rapid Barcoding library kit that allows universal SARS-CoV-2 genome sequencing. This primer set is designed to set up any variants of the primers pool for whole-genome sequencing of SARS-CoV-2 using single- or double-tiled amplicons from 1.2 to 4.8 kb with the Oxford Nanopore. This multiplexed set of primers is also applicable for tasks like targeted SARS-CoV-2 genome sequencing. We proposed here an optimized protocol to synthesize cDNA using Maxima H Minus Reverse Transcriptase with a set of SARS-CoV-2 specific primers, which has high yields of cDNA template for RNA and is capable of long-length cDNA synthesis from a wide range of RNA amounts and quality. The proposed protocol allows whole-genome sequencing of the SARS-CoV-2 virus with tiled amplicons up to 4.8 kb on low-titer virus samples and even where RNA degradation has occurred. This protocol reduces the time and cost from RNA to genome sequence compared to the Midnight multiplex PCR method for SARS-CoV-2 genome sequencing using the Oxford Nanopore. |
format | Online Article Text |
id | pubmed-10293217 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-102932172023-06-28 Universal whole-genome Oxford nanopore sequencing of SARS-CoV-2 using tiled amplicons Kalendar, Ruslan Kairov, Ulykbek Karabayev, Daniyar Aitkulova, Akbota Tynyshtykbayeva, Nuray Daniyarov, Asset Otarbay, Zhenis Rakhimova, Saule Akilzhanova, Ainur Sarbassov, Dos Sci Rep Article We developed a comprehensive multiplexed set of primers adapted for the Oxford Nanopore Rapid Barcoding library kit that allows universal SARS-CoV-2 genome sequencing. This primer set is designed to set up any variants of the primers pool for whole-genome sequencing of SARS-CoV-2 using single- or double-tiled amplicons from 1.2 to 4.8 kb with the Oxford Nanopore. This multiplexed set of primers is also applicable for tasks like targeted SARS-CoV-2 genome sequencing. We proposed here an optimized protocol to synthesize cDNA using Maxima H Minus Reverse Transcriptase with a set of SARS-CoV-2 specific primers, which has high yields of cDNA template for RNA and is capable of long-length cDNA synthesis from a wide range of RNA amounts and quality. The proposed protocol allows whole-genome sequencing of the SARS-CoV-2 virus with tiled amplicons up to 4.8 kb on low-titer virus samples and even where RNA degradation has occurred. This protocol reduces the time and cost from RNA to genome sequence compared to the Midnight multiplex PCR method for SARS-CoV-2 genome sequencing using the Oxford Nanopore. Nature Publishing Group UK 2023-06-26 /pmc/articles/PMC10293217/ /pubmed/37365249 http://dx.doi.org/10.1038/s41598-023-37588-x Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/ Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Kalendar, Ruslan Kairov, Ulykbek Karabayev, Daniyar Aitkulova, Akbota Tynyshtykbayeva, Nuray Daniyarov, Asset Otarbay, Zhenis Rakhimova, Saule Akilzhanova, Ainur Sarbassov, Dos Universal whole-genome Oxford nanopore sequencing of SARS-CoV-2 using tiled amplicons |
title | Universal whole-genome Oxford nanopore sequencing of SARS-CoV-2 using tiled amplicons |
title_full | Universal whole-genome Oxford nanopore sequencing of SARS-CoV-2 using tiled amplicons |
title_fullStr | Universal whole-genome Oxford nanopore sequencing of SARS-CoV-2 using tiled amplicons |
title_full_unstemmed | Universal whole-genome Oxford nanopore sequencing of SARS-CoV-2 using tiled amplicons |
title_short | Universal whole-genome Oxford nanopore sequencing of SARS-CoV-2 using tiled amplicons |
title_sort | universal whole-genome oxford nanopore sequencing of sars-cov-2 using tiled amplicons |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10293217/ https://www.ncbi.nlm.nih.gov/pubmed/37365249 http://dx.doi.org/10.1038/s41598-023-37588-x |
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