Evaluation of an optimized protocol and Illumina ARTIC V4 primer pool for sequencing of SARS-CoV-2 using COVIDSeq™ and DRAGEN™ COVID Lineage App workflow
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Abstract
Next-Generation Sequencing based genomic surveillance has been widely implemented for identification and tracking of emerging SARS-CoV-2 variants to guide the Public Health response to the COVID-19 pandemic. Amplicon-based assays, such as the Illumina ® COVIDSeq™ Test (RUO) and COVIDSeq Assay (RUO), enable scalable sequencing of SARS-CoV-2, leveraging V3 and V4 primer designs from the ARTIC community and DRAGEN™ COVID Lineage App analysis available on Illumina BaseSpace™. We report here a comparison of COVIDSeq performance for SARS-CoV-2 genome reporting using the ARTIC V3 based primer pool (including primers for human control genes) that is provided with the COVIDSeq kit versus the ARTIC V4 based Illumina COVIDSeq V4 primer pool, using an optimized protocol and DRAGEN COVID Lineage App analysis. The data indicates that both primer pools enable robust reporting of SARS-CoV-2 variants. The Illumina COVIDSeq V4 primer pool has superior performance for SARS-CoV-2 genome reporting, particularly in samples with low virus load, and is therefore the recommended primer pool for genomic surveillance of SARS-CoV-2 for research use using COVIDSeq.
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SciScore for 10.1101/2022.01.07.475443: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources The King Fisher™ Flex Magnetic Particle Processor with 96 Deep-Well head and the MagMAX™ Viral/Pathogen II Nucleic Acid Isolation Kit was used for high throughput extraction of patient specimens, and the TaqPath™ COVID-19 Combo Kit was used for the detection of SARS-CoV-2 ORF1ab, N protein, and S protein genes by real-time RT-PCR using Applied Biosystems® QuantStudio™ 7 Flex Real Time PCR instruments, QuantStudio™ Real Time PCR Software v1.3, and Applied Biosystems® COVID-19 Interpretive Software. Applied …SciScore for 10.1101/2022.01.07.475443: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources The King Fisher™ Flex Magnetic Particle Processor with 96 Deep-Well head and the MagMAX™ Viral/Pathogen II Nucleic Acid Isolation Kit was used for high throughput extraction of patient specimens, and the TaqPath™ COVID-19 Combo Kit was used for the detection of SARS-CoV-2 ORF1ab, N protein, and S protein genes by real-time RT-PCR using Applied Biosystems® QuantStudio™ 7 Flex Real Time PCR instruments, QuantStudio™ Real Time PCR Software v1.3, and Applied Biosystems® COVID-19 Interpretive Software. Applied Biosystems®suggested: (Applied Biosystems, RRID:SCR_005039)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- No funding statement was detected.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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