SARS-CoV-2 Variant Identification Using a Genome Tiling Array and Genotyping Probes

Shimada, Ryota; Alden, Emily N.; Hoff, Kendall; Ding, Dun; Sun, Jiayi; Halász, Ádám; Zhou, Wei; Edwards, Jeremy S.

doi:10.1101/2021.05.11.443659

Cited by 3 publications

(6 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The tiling array is identical to the previously described DNA chip design (Centrillion Technologies) 11,13,14 . Nucleic acid extraction was performed using the Magnetic Bead 96 Viral Isolation Kit (Bioperfectus Technologies).…”

Section: Methodsmentioning

confidence: 99%

“…Using the total number of high‐quality calls as the reference call count, the number of true variant calls identified correctly, and the number of incorrect identified calls, accuracy calculations are performed. Coverage is calculated by the total number of calls (reference base or variant calls) divided by the size of the SARS‐CoV‐2 reference genome 23 . Sequence alignment was performed using Geneious Software.…”

Section: Methodsmentioning

confidence: 99%

“…The tiling array is identical to the previously described DNA chip design (Centrillion Technologies). 11,13,14 hybridization, the chips were washed in Wash A (2×SSC, Sodium Citrate Buffer, 0.1% TWEEN-20) at room temperature for 2 min and then transferred into Wash B (0.5×SSC, 0.1% TWEEN-20) at 30°C for 5 min. The chips were stained with 0.02 mg/mL Cy3-Streptavidin in 4×SSC at room temperature for 5 min before being washed with 4×SSC at room temperature for 5 min.…”

Section: Sample Preparation For Sars-cov-2 Tiling Arraymentioning

confidence: 99%

“…divided by the size of the SARS-CoV-2 reference genome. 23 Sequence alignment was performed using Geneious Software.…”

Section: Bioinformatic Analysis For Sars-cov-2 Illumina Sequencingmentioning

confidence: 99%

See 3 more Smart Citations

Application of whole‐genome tiling array at Shanghai port, China: An alternative method for SARS‐CoV‐2 surveillance

Liu,

Wang,

Mao

et al. 2023

Journal of Medical Virology

View full text Add to dashboard Cite

The ongoing coronavirus disease 2019 (COVID‐19) pandemic, driven by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), highlights the critical role of genomic surveillance in tracking rapidly spreading viruses and their evolving lineages. The emergence of the SARS‐CoV‐2 tiling array, a comprehensive tool capable of capturing the entire viral genome, has presented a promising avenue for variants. This study introduces the SARS‐CoV‐2 tiling array as a novel method for port inspection. Using next‐generation sequencing as a benchmark, 35 positive samples underwent sequencing through both methodologies, including the Alpha variant (B.1.1.7), Delta variants (AY.120, AY.122, AY.23.1), and Omicron variants (BA.1, BA.2, BA.2.75, BA.4, BA.5, BE.1, BF.7, BN.1, BQ.1, XBB.1) within the sample set. The whole‐genome tiling array demonstrated successful identification of various sublineages of SARS‐CoV‐2. The average sequencing coverage rates were 99.22% (96.82%−99.92%) for the whole‐genome tiling array and 98.56% (92.81%−99.59%) for Illumina sequencing, respectively. The match rates of these two methods ranged from 92.81%−99.59%, with an average rate of 98.56%. Among the benefits of the whole‐genome tiling array are its cost‐effectiveness and equipment simplification, making it particularly suitable for identifying SARS‐CoV‐2 variants in the front‐line inspection department. The aforementioned findings provide valuable insights into the surveillance of COVID‐19 and present a pragmatic solution for improving quarantine measures at entry points.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Sample Preparation For Sars-cov-2 Tiling Arraymentioning

confidence: 99%

“…divided by the size of the SARS-CoV-2 reference genome. 23 Sequence alignment was performed using Geneious Software.…”

Section: Bioinformatic Analysis For Sars-cov-2 Illumina Sequencingmentioning

confidence: 99%

See 2 more Smart Citations

Application of whole‐genome tiling array at Shanghai port, China: An alternative method for SARS‐CoV‐2 surveillance

Liu,

Wang,

Mao

et al. 2023

Journal of Medical Virology

View full text Add to dashboard Cite

show abstract

“…Recognizing the limitations to throughput for the BBP-RMAv.2 suggests that using it as a supplemental test for many different screening tests may be its initial role. Modifications to the platform can increase throughput and reduce cost (Shimada et al, 2021), such that the primers and tiles that were demonstrated effective here could be more practically applied.…”

Section: Discussionmentioning

confidence: 99%

Table1.DOC

View full text Add to dashboard Cite

Multiplex detection and identification of viral, bacterial, and protozoan pathogens in human blood and plasma using an expanded high-density resequencing microarray platform

Kourout,

Espich,

Fisher

et al. 2024

Front. Mol. Biosci.

View full text Add to dashboard Cite

Introduction: Nucleic acid tests for blood donor screening have improved the safety of the blood supply; however, increasing numbers of emerging pathogen tests are burdensome. Multiplex testing platforms are a potential solution.Methods: The Blood Borne Pathogen Resequencing Microarray Expanded (BBP-RMAv.2) can perform multiplex detection and identification of 80 viruses, bacteria and parasites. This study evaluated pathogen detection in human blood or plasma. Samples spiked with selected pathogens, each with one of 6 viruses, 2 bacteria and 5 protozoans were tested on this platform. The nucleic acids were extracted, amplified using multiplexed sets of primers, and hybridized to a microarray. The reported sequences were aligned to a database to identify the pathogen. To directly compare the microarray to an emerging molecular approach, the amplified nucleic acids were also submitted to nanopore next generation sequencing (NGS).Results: The BBP-RMAv.2 detected viral pathogens at a concentration as low as 100 copies/ml and a range of concentrations from 1,000 to 100,000 copies/ml for all the spiked pathogens. Coded specimens were identified correctly demonstrating the effectiveness of the platform. The nanopore sequencing correctly identified most samples and the results of the two platforms were compared.Discussion: These results indicated that the BBP-RMAv.2 could be employed for multiplex detection with potential for use in blood safety or disease diagnosis. The NGS was nearly as effective at identifying pathogens in blood and performed better than BBP-RMAv.2 at identifying pathogen-negative samples.

show abstract

SARS-CoV-2 Variant Identification Using a Genome Tiling Array and Genotyping Probes

Cited by 3 publications

References 19 publications

Application of whole‐genome tiling array at Shanghai port, China: An alternative method for SARS‐CoV‐2 surveillance

Application of whole‐genome tiling array at Shanghai port, China: An alternative method for SARS‐CoV‐2 surveillance

Table1.DOC

Multiplex detection and identification of viral, bacterial, and protozoan pathogens in human blood and plasma using an expanded high-density resequencing microarray platform

Contact Info

Product

Resources

About