Genemarkers LLC and Swift Biosciences Detect Unexpected Variant from COVID-19 S Gene Dropout Samples from Kalamazoo, MI
ANN ARBOR, Mich (February 17, 2021) Genemarkers LLC, leaders in genomic research from Kalamazoo, MI and Swift Biosciences, pioneers in the development of DNA and RNA library preparation kits for Next-Generation Sequencing (NGS) systems in Ann Arbor, MI, collaborated together to detect mutations and variants from COVID-19 samples sourced in Kalamazoo, MI. Genemarkers Senior Scientist Dr. Rishabh Kala was aware of the presence of “the UK variant” (B.1.1.7) in Michigan and called upon Swift Biosciences to use their highly sensitive Next-Generation Sequencing (NGS) Swift Normalase® Amplicon SARS-CoV-2 Panel (SNAP) and S Gene Panel (SNAP) to validate the findings from their current assay for samples with dropout in the S Gene that they believed to be indicative of the UK variant.
Genemarkers’ CLIA lab, which performs routine COVID-19 testing, de-identified the samples prior to sending to Swift. The team at Swift performed reverse transcription using Superscript® IV to generate cDNA as the input material to create libraries with both the SNAP SARS-CoV-2 Extended Genomic coverage panel and the SNAP S gene panel. . Sequencing data was analyzed by Dr. Sukhinder Sandhu, Head of Bioinformatics at Swift, using the Swift Bioinformatic pipeline for variant calling. Swift’s findings show that 6 of the 7 samples had mutations consistent with the UK variant and one sample was an unexpected variant that did not have identifiers for the UK, South African, CA or Brazilian mutation. The full genome sequencing data was used to determine that this unexpected strain belonged to the 20C clade, specifically B.1.375. The mutations indicative of 20C (C1059T and G25563T) were both present. The B.1.3.75 and B.1.1.7 strains share a mutation in the S Gene, Del69-70, which is likely the explanation of the S gene dropout. Both the SARS-CoV-2 genome panel and the S Gene panel produced results that were consistent and accurate.
This data underscores the importance of full genome sequencing in disease tracking and surveillance. The assumption that any drop in S Gene signal was due to the UK variant would have led to inaccurate reporting and confused variant tracking.
“It is extremely important to the research community to understand all of the variants in order to guide vaccine development and mitigation strategies,” said Dr. Kala. “As the virus spreads throughout the community the greater the chance it has to mutate. We know that the UK variant is more contagious and now we will begin work to understand the implications of the new mutation.”
About Genemarkers, LLC
Genemarkers is a leader in applying state-of-the-art genomics technologies to personal care, nutritional and pharmaceutical research. Working with a wide range of customers, Genemarkers’ gene expression profiling and genotyping services help identify biomarkers and elucidate biological mechanisms of action for new products. The data is used to enhance the product development process and validates the efficacy of topical products.
About Swift Biosciences
Swift Biosciences develops and commercializes NGS Library Preparation Kits to advance research into improvements in the health of individuals and their communities worldwide, specifically in the fight against cancer and management of inherited diseases. Our research use only (RUO) tools are used in areas such as agrigenomics, infectious disease research, metagenomics, and the pharmaceutical industry. Swift Library Prep Kits maximize data output, provide the most comprehensive coverage available on the market, and reduce sequencing costs. Our products normalize NGS libraries for applications including Liquid Biopsy (circulating, cell-free DNA), Methylation Sequencing, Whole Genome Sequencing, Exome Sequencing, Transcriptome Sequencing, and Chromatin studies from low input quantities and Formalin-Fixed, Paraffin-Embedded samples.
For more information, visit SwiftBioSci.com and follow Swift Biosciences on Twitter (@SwiftBioSci).
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