The companies have developed the SARS-CoV-2 Next-Generation Sequencing (NGS) Assay, an NGS-based assay for research use only (RUO). The SARS-CoV-2 NGS RUO Assay is a highly sensitive nucleic acid hybridization capture-based assay used for the detection, characterization, and environmental monitoring of the SARS-CoV-2 virus. It utilizes Twist Bioscience’s unique ability to rapidly develop virus-specific panels by DNA synthesis and Biotia’s comprehensive data analysis software and reporting capabilities.
The SARS-CoV-2 NGS Assay was validated on a NextSeq sequencer and identifies all SARS-CoV-2 nucleic acid sequences, to allow for surveillance of how the genetic sequence of the virus is changing. In contrast, a majority of SARS-CoV-2 tests based on polymerase chain reaction (PCR) only identify limited genetic markers of the virus. A recent study1 compared the performance of three different commercially available NGS library preparation kits confirming that hybridization capture results in more even coverage across all sequences in a sample when compared to PCR-based NGS assays. In addition, the SARS-CoV-2 NGS Assay reports the full sequence of the virus, enabling improved understanding of mutations, genetic variations and the evolution of the virus as it is transmitted.
“While there are many available high-throughput diagnostic tests available for covid-19, our solution provides sequence data that enables researchers the ability to sequence and surveil the evolution of mutations in the virus over time and geography,” says Emily M. Leproust, PhD, CEO and co-founder of Twist Bioscience. “Importantly, while many labs are conducting individual sequencing runs for each patient sample, this assay and the accompanying software provide a way to batch about 100 patient samples together, providing actionable information that can then be used to inform public health particularly as we see second and third waves of covid escalating.”
“We are fortunate to be in a position where we can devote our time and resources to fight this global pandemic,” says Niamh O’Hara, PhD, CEO and co-founder of Biotia. “This novel and insightful covid-19 solution is an important step to make NGS-based infectious disease surveillance more widely available and to advance covid-19 research and control.”
Biotia presented data from the assay at the Infectious Disease Week (IDWeek) 2020 Annual Meeting that identify 124 genetic mutations not previously described, including 26 in the functionally important spike protein of SARS-CoV-2. The end-to-end solution was validated on 120 clinical samples (60 positive, 60 negative), and confirmed that the SARS-CoV-2 NGS Assay powered by the COVID-DX Software could be used to detect viral RNA in laboratory research settings. It also provided insight into genetic variants to track transmission, identify risk, and predict outcome and therapeutic response. [Nagy-Szakal et al., SARS-CoV-2 NGS Assay Powered by Biotia COVID-DX Software, IDWeek 2020]
“This test spans both diagnostic methods and vaccine research,” says Christopher Mason, PhD, co-founder of Biotia, “We believe this end-to-end solution brings needed tools into the fight against covid-19, as well as pioneering these capture methods for tracking other pathogens in the future.”
About the Solution
The SARS-CoV-2 NGS Assay is an RUO end-to-end solution intended for the quantitative detection of the SARS-CoV-2 virus from nasopharyngeal (NP), oropharyngeal (OP), anterior nasal, and mid-turbinate nasal swabs as well as from nasopharyngeal wash/aspirates, nasal aspirates, and bronchoalveolar lavage (BAL) specimens from individuals. The SARS-CoV-2 NGS Assay, which includes Twist Bioscience’s SARS-CoV-2 synthetic RNA controls, detects all strains of SARS-CoV-2 in samples with as few as 800 viral copies per milliliter
The complementary Biotia COVID-DX software provides an RUO report including the presence or absence of SARS-CoV-2 virus, the full sequence of the virus, genetic variants and phylogenetic analysis. FASTQ files (sequencing output) can be generated in laboratories nationwide and submitted to Biotia COVID-DX (v1.0), a cloud-based software to generate RUO reports. Access to the Biotia COVID-DX software is provided through a unique order number emailed to a researcher that includes credits for each kit purchased.
- Klempt P, Brož P, Kašný M, Novotný A, Kvapilová K, Kvapil P. Performance of Targeted Library Preparation Solutions for SARS-CoV-2 Whole Genome Analysis. Diagnostics (Basel). 2020;10(10):E769. Published 2020 Sep 29. doi:10.3390/diagnostics10100769