The SARS-CoV-2 NGS assay is a in vitro diagnostic test, a highly sensitive assay based on nucleic acid hybridization based on the detection of SARS-CoV-2 RNA.
The SARS-CoV-2 NGS assay can analyze the entire RNA virus sequence to determine the presence or absence of the virus. In addition, the software analyzes the RNA sequence in an optional research-use-only report (RUO) in order to detect genetic variants and lineages of SARS-CoV-2.1 The hybridization capture-based approach used in this assay maximizes the number of genetic variants identified where other sequencing methods may miss mutations in specific regions.
New mutations in the SARS-CoV-2 virus continue to accumulate and circulate around the world, leading to genetic variants of concern that may alter the communicability or effectiveness of the vaccine, including the most recent B.1.1.7, B.1.351, and P. .1 lineages originally found in the UK, South Africa and Brazil. In view of these new variants in particular, this capture-based method is an important new tool for identifying, sequencing and monitoring COVID-19.
The World Health Organization’s genome sequencing for SARS-CoV-2 published on January 8, 2021 states: “One advantage of using a capture-based approach over a PCR amplicon-based approach is that capture-based approaches tolerate sequence differences can probe sequences of 10–20%. This is higher than the mismatch tolerated by PCR, where such a deviation from the primer sequences would lead to a high risk of amplicon failure. Capture-based approaches can therefore be used to successfully enrich relatively different SARS-CoV-2 sequences. “
“While there are many high-throughput diagnostic tests available for COVID-19, our solution allows doctors and researchers to track and monitor the evolution of mutations in the virus over time and geographically. This is especially important right now as more variants are identified that are more contagious, ”said Emily M. Leproust, Ph.D., CEO and co-founder of Twist Bioscience. “While many laboratories perform individual sequencing runs for each patient sample, this assay and associated software provide a way to aggregate approximately 100 samples and provide actionable information that can then be used to inform public health and clinical decisions.”
The assay leverages Twist Bioscience’s unique ability to rapidly develop virus-specific panels through DNA synthesis and Biotia’s comprehensive data analysis software and reporting capabilities. The SARS-CoV-2 NGS assay has been validated on a NextSeq® 550 sequencing system. Because the assay analyzes the complete sequence data, the test reduces the chance of a false negative result. In contrast, the majority of SARS-CoV-2 tests, which are based on the polymerase chain reaction (PCR), only identify limited genetic markers of the virus.
The complete sequence of the virus is described in the separate and free RUO report, which enables a better understanding of the mutations, genetic variability and evolution of the virus during its transmission. A recently published form on MedRxiv that was submitted for peer review provides details of the results of the NGS SARS-CoV-2 assay using the COVID-DX solution to detect the virus and its genetic variants.
“As SARS-CoV-2 evolves, the need for insightful research tools that use NGS and evolutionary principles has become evident,” commented Dr. Niamh O’Hara, CEO and Co-Founder of Biotia is also significantly expanding clinical testing options and bringing new technologies to patients. “
“This test opens the door to a new diagnostic tool and can also guide vaccine research because it detects viral variants so well,” said Christopher Mason, Ph.D., co-founder of Biotia EUA for our test, which has the tools needed in the fight against COVID-19 and pioneering these trapping methods to track other pathogens in the future. “
About the test and the interface
The SARS-CoV-2 NGS assay is a in vitro Diagnostic test for the qualitative identification of the SARS-CoV-2 virus from nasopharyngeal (NP), oropharyngeal (OP), anterior nasal and middle turbinate nasal swabs, nasopharyngeal washing / aspiration, nasal washing / aspiration and bronchoalveolar lavage (BAL) samples who are suspected of having COVID-19 by their healthcare provider. The SARS-CoV-2-NGS assay, which includes Twist Bioscience’s SARS-CoV-2 synthetic RNA controls, as well as Biotia COVID-DX software, which produces a clinical report and an RUO report, cover all of this Virus genome and identify all SARS strains -CoV-2 in samples with only 800 virus copies per milliliter.
The complementary Biotia COVID-DX software offers a clinically oriented report that includes the presence or absence of the SARS-CoV-2 virus. FASTQ (sequencing output) files can be created in certified clinical laboratories and sent to Biotia COVID-DX (v1.0), a cloud-based software, to generate clinical reports. Biotia COVID-DX software is accessed through a unique order number that is emailed to a clinician or researcher and includes credits for each kit purchased.
The SARS-CoV-2 NGS assay and the Biotia COVID-DX software are limited to laboratories certified to the Clinical Laboratory Improvement Amendments (CLIA) to perform highly complex tests. The SARS-CoV-2 NGS Assay is intended for use by Qualified and trained clinical laboratory personnel specifically instructed and trained in the use of the Illumina NextSeq 500/550 / 550Dx Sequencing System, NGS workflows, and in vitro diagnostic procedures. The SARS-CoV-2 NGS assay may only be used within the framework of the emergency approval of the Food and Drug Administration. This test will be available for purchase in the coming weeks.