SARS-CoV-2 Whole-Genome Sequencing by Ion S5 Technology—Challenges, Protocol Optimization and Success Rates for Different Strains

Szargut, Maria; Cytacka, Sandra; Serwin, Karol; Urbańska, Anna; Gastineau, Romain; Parczewski, Miłosz; Ossowski, Andrzej

doi:10.3390/v14061230

Cited by 2 publications

(2 citation statements)

References 44 publications

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“…It is, therefore, signi cant to note that standardising assembly and analysis software allows for improved comparison of the data generated by the different platforms and data analysed by different software. Nonetheless, this study complements previous research investigating the e cacy of Ion Torrent and Illumina platforms for sequencing viral pathogens (23,24,50).…”

Section: Discussionsupporting

confidence: 73%

Comparing SARS-CoV-2 sequencing methodologies during early phase detection of the Delta variant in South Africa

Ramphal

Tshiabuila

Ramphal

et al. 2023

Preprint

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Background: Genomic surveillance, with the aid of next-generation sequencing (NGS) technologies, revolutionized the SARS-CoV-2 pandemic. Coupled with high-performance analysis software, methodologies such as the Ion Torrent S5 and Illumina MiSeq dramatically improved the genomic surveillance capacity within South Africa during the height of the pandemic. Using de-identified remnant samples collected from Eastern Cape and analysis software, Genome Detective and NextClade, we compared the sequencing process, genomic coverage, quantification of mutations, and clade classification from sequence data generated by these two common “benchtop” NGS platforms. Results: Sequence data analysis revealed success rates of 175/183 (96%) and 172/183 (94%) on the Ion Torrent S5 and Illumina MiSeq, respectively. Internal quality metrics were assessed in terms of genomic coverage (>80%) and the number of mutations identified (<100). A greater number of higher-genomic coverage sequences were generated on the Ion Torrent S5 (99%) than on the Illumina MiSeq (80%) and <100 mutations was obtained by both platforms. Ion Torrent S5 generated high coverage sequences from samples having a broader range of viral loads (VL) compared to the Illumina MiSeq, which was less successful in sequencing samples with lower viral loads. Clade assignments were comparable across platforms which accurately differentiated between Beta (<45%) and Delta (≤30%) VOCs. A disparity in clade assignment was observed in <10% of sequences due to poor coverage obtained on the Illumina MiSeq, followed by a failure rate of ≤6% across the two platforms. Manual library preparation found both methods similar in terms of sample processing, handling of larger sample quantities, and clade assignment for SARS-CoV-2. Variability between the Ion Torrent S5 and Illumina MiSeq was observed in sequencing run duration (3,5 hrs vs 36 hrs), sequencing process (semi-automation vs manual), genomic coverage (99% vs 80%), and viral load requirements (broad range vs high VL). Conclusion: The Illumina MiSeq and Ion Torrent S5 are both reliable platforms capable of performing WGS with the use of amplicons and providing specific, accurate, and high throughput analysis of the SARS-CoV-2 whole viral genomes. Both sequencing platforms are feasible platforms for the genomic surveillance of SARS-CoV-2, each with its specific advantages and trade-offs.

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Section: Discussionsupporting

confidence: 73%

Comparing SARS-CoV-2 sequencing methodologies during early phase detection of the Delta variant in South Africa

Ramphal

Tshiabuila

Ramphal

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…It is, therefore, important to note that standardising assembly and analysis software allows for improved comparison of the data generated by the different platforms and data analysed by different software. Nonetheless, this study complements previous research investigating the efficacy of Ion Torrent and Illumina platforms for sequencing viral pathogens [23,24,52].…”

Section: Discussionsupporting

confidence: 65%

Reflective Evaluation of Next-Generation Sequencing Data during Early Phase Detection of the Delta Variant

RAMPHAL,

Tshiabuila,

Ramphal

et al. 2024

OBM Genet

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During the SARS-CoV-2 pandemic, next-generation sequencing (NGS) technologies like the Ion Torrent S5 and Illumina MiSeq, alongside advanced software, improved genomic surveillance in South Africa. This study analysed anonymized samples from the Eastern Cape using Genome Detective and NextClade, showing Ion Torrent S5 and Illumina MiSeq success rates of 96% and 94%, respectively. The study focused on genomic coverage (above 80%) and mutation detection (below 100), with the Ion Torrent S5 achieving 99% coverage compared to Illumina MiSeq's 80%, likely due to different primers used in amplification. The Ion Torrent S5 was more effective in sequencing varied viral loads, whereas Illumina MiSeq had difficulties with lower loads. Both platforms were adept at identifying clades, successfully differentiating between Beta (<45%) and Delta variants (<30%), despite minor discrepancies in assignments due to Illumina MiSeq's lower coverage, leading to a failure rate of up to 6%. Manual library preparation showed similar sample processing and clade identification capabilities for both platforms. However, differences in sequencing duration (3.5 vs. 36 hours), automation level, genomic coverage (80% vs. 99%), and viral load compatibility were noted, highlighting each platform's unique advantages and challenges in SARS-CoV-2 genomic surveillance. In conclusion, the Illumina MiSeq and Ion Torrent S5 platforms are both efficacious in executing whole-genome sequencing (WGS) via amplicons, facilitating precise, accurate, and high-throughput examinations of SARS-CoV-2 viral genomes. However, it is important to note the existence of disparities in the quality of data produced by each platform. Each system offers unique benefits and limitations, rendering them viable choices for the genomic surveillance of SARS-CoV-2.

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SARS-CoV-2 Whole-Genome Sequencing by Ion S5 Technology—Challenges, Protocol Optimization and Success Rates for Different Strains

Cited by 2 publications

References 44 publications

Comparing SARS-CoV-2 sequencing methodologies during early phase detection of the Delta variant in South Africa

Comparing SARS-CoV-2 sequencing methodologies during early phase detection of the Delta variant in South Africa

Reflective Evaluation of Next-Generation Sequencing Data during Early Phase Detection of the Delta Variant

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