SARS-CoV-2
Genetic Fingerprinting

Profile Viral Genome and Subgenomic RNA
Directly from Samples

DeepMARK™ is a SARS-CoV-2 next-generation sequencing (NGS) test that directly profiles and analyses both genomic RNA and subgenomic RNA data from the same sequencing run. Our proprietary error-correcting NGS technology AmpliMARK™ achieves >99% SARS-CoV-2 genome coverage while eliminating routine sequencing errors.

 

Features Applications
  1. Detects both genomic RNA and subgenomic RNA (sgRNA)
  2. Quantifies viral replication without need for viral culture
  3. Identifies haplotypes and quasispecies,
  4. Identifies canonical and non-canonical fusion sgRNA
  1. Advance epidemiological research on COVID-19
  2. Evaluate transmissibility in patients
  3. Enable accurate surveillance and contact tracing
  4. Identify novel targets for drug and vaccine development

 

Pinpointing Unseen Transmission Paths to Help Link Cases

13 cases from one community were analyzed. Individual viral genomes were visualized using a phylogenetic tree to identify transmission patterns. Viral genomes that are more closely related could be accurately linked to their physical locations in each building. The data from DeepMARK™ further differentiates the patients into specific clusters, indicating multiple transmission paths within a single community.

 

Credit to: Teo AKJ, Hsu LY, et al. (manuscript in preparation) 2020.

Technical Specifications

Workflow

RNA can be extracted from clinical specimens such as nasopharyngeal swabs (NP), oropharyngeal swabs (OP) and saliva specimens. Following cDNA conversion and library preparation, sequencing is carried out on an Illumina®-based platform. FASTQ files generated from the sequencer are then uploaded into the Lucence DeepMARK™ pipeline for automated analysis.

 

Depth of Genome Coverage

Clinical Evaluation

Clinical performance of the DeepMARK™ was evaluated in comparison with the CDC laboratory-developed test using the RT-PCR method for the detection of SARS-CoV-2 in clinical samples. The RT-PCR assay is based on primers from the CDC test (2019-nCov CDC test). The positive and negative percent agreement was calculated in relation to the RT-PCR method.

 

 

Method Multiplex amplicon-based next-generation sequencing
Sample Types Accepted RNA from Clinical Specimens or Viral Culture
System Compatibility Illumina® Platforms
Kit Components Box 1: Reverse Transcription Module
Box 2: Polymerase Chain Reaction Module
Box 3: Library Amplification Module 
Storage Temperature -20 °C
Kit Size (Reactions) 20 (Cat. No. DM-SC2-001-20)
50 (Cat. No. DM-SC2-001-50)
Limit of Detection (LOD) 50 copies/mL

Intended Use

DeepMARK™ is a next-generation sequencing (NGS) assay for clinical research applications, for the qualitative analysis of SARS-CoV-2 RNA. Positive results are indicative of the presence of SARS-CoV-2 RNA in the research specimen.

 

For Research Use Only. DeepMARK™ is developed and designed exclusively for research use only, and is manufactured in an ISO-13485-compliant facility. It is not a test for any disease. Collection and processing of samples for any purpose shall be conducted in accordance with local healthcare regulations. Lucence is not responsible for any injury, loss or damages arising from use outside intended use.

 

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