Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing.
The global pandemic caused by SARS-CoV-2 has increased the demand for scalable sequencing and diagnostic methods, especially for genomic surveillance. Although next-generation sequencing has enabled large-scale genomic surveillance, the ability to sequence SARS-CoV-2 in some settings has been limite...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2023-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0283219 |
| _version_ | 1797828065073561600 |
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| author | Sureshnee Pillay James Emmanuel San Derek Tshiabuila Yeshnee Naidoo Yusasha Pillay Akhil Maharaj Ugochukwu J Anyaneji Eduan Wilkinson Houriiyah Tegally Richard J Lessells Cheryl Baxter Tulio de Oliveira Jennifer Giandhari |
| author_facet | Sureshnee Pillay James Emmanuel San Derek Tshiabuila Yeshnee Naidoo Yusasha Pillay Akhil Maharaj Ugochukwu J Anyaneji Eduan Wilkinson Houriiyah Tegally Richard J Lessells Cheryl Baxter Tulio de Oliveira Jennifer Giandhari |
| author_sort | Sureshnee Pillay |
| collection | DOAJ |
| description | The global pandemic caused by SARS-CoV-2 has increased the demand for scalable sequencing and diagnostic methods, especially for genomic surveillance. Although next-generation sequencing has enabled large-scale genomic surveillance, the ability to sequence SARS-CoV-2 in some settings has been limited by the cost of sequencing kits and the time-consuming preparations of sequencing libraries. We compared the sequencing outcomes, cost and turn-around times obtained using the standard Illumina DNA Prep kit protocol to three modified protocols with fewer clean-up steps and different reagent volumes (full volume, half volume, one-tenth volume). We processed a single run of 47 samples under each protocol and compared the yield and mean sequence coverage. The sequencing success rate and quality for the four different reactions were as follows: the full reaction was 98.2%, the one-tenth reaction was 98.0%, the full rapid reaction was 97.5% and the half-reaction, was 97.1%. As a result, uniformity of sequence quality indicated that libraries were not affected by the change in protocol. The cost of sequencing was reduced approximately seven-fold and the time taken to prepare the library was reduced from 6.5 hours to 3 hours. The sequencing results obtained using the miniaturised volumes showed comparability to the results obtained using full volumes as described by the manufacturer. The adaptation of the protocol represents a lower-cost, streamlined approach for SARS-CoV-2 sequencing, which can be used to produce genomic data quickly and more affordably, especially in resource-constrained settings. |
| first_indexed | 2024-04-09T12:58:25Z |
| format | Article |
| id | doaj.art-a905d510469b4341bedf460971334fbc |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-09T12:58:25Z |
| publishDate | 2023-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-a905d510469b4341bedf460971334fbc2023-05-13T05:31:35ZengPublic Library of Science (PLoS)PLoS ONE1932-62032023-01-01184e028321910.1371/journal.pone.0283219Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing.Sureshnee PillayJames Emmanuel SanDerek TshiabuilaYeshnee NaidooYusasha PillayAkhil MaharajUgochukwu J AnyanejiEduan WilkinsonHouriiyah TegallyRichard J LessellsCheryl BaxterTulio de OliveiraJennifer GiandhariThe global pandemic caused by SARS-CoV-2 has increased the demand for scalable sequencing and diagnostic methods, especially for genomic surveillance. Although next-generation sequencing has enabled large-scale genomic surveillance, the ability to sequence SARS-CoV-2 in some settings has been limited by the cost of sequencing kits and the time-consuming preparations of sequencing libraries. We compared the sequencing outcomes, cost and turn-around times obtained using the standard Illumina DNA Prep kit protocol to three modified protocols with fewer clean-up steps and different reagent volumes (full volume, half volume, one-tenth volume). We processed a single run of 47 samples under each protocol and compared the yield and mean sequence coverage. The sequencing success rate and quality for the four different reactions were as follows: the full reaction was 98.2%, the one-tenth reaction was 98.0%, the full rapid reaction was 97.5% and the half-reaction, was 97.1%. As a result, uniformity of sequence quality indicated that libraries were not affected by the change in protocol. The cost of sequencing was reduced approximately seven-fold and the time taken to prepare the library was reduced from 6.5 hours to 3 hours. The sequencing results obtained using the miniaturised volumes showed comparability to the results obtained using full volumes as described by the manufacturer. The adaptation of the protocol represents a lower-cost, streamlined approach for SARS-CoV-2 sequencing, which can be used to produce genomic data quickly and more affordably, especially in resource-constrained settings.https://doi.org/10.1371/journal.pone.0283219 |
| spellingShingle | Sureshnee Pillay James Emmanuel San Derek Tshiabuila Yeshnee Naidoo Yusasha Pillay Akhil Maharaj Ugochukwu J Anyaneji Eduan Wilkinson Houriiyah Tegally Richard J Lessells Cheryl Baxter Tulio de Oliveira Jennifer Giandhari Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing. PLoS ONE |
| title | Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing. |
| title_full | Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing. |
| title_fullStr | Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing. |
| title_full_unstemmed | Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing. |
| title_short | Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing. |
| title_sort | evaluation of miniaturized illumina dna preparation protocols for sars cov 2 whole genome sequencing |
| url | https://doi.org/10.1371/journal.pone.0283219 |
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