Solutions for sensitive viral detection

Your partner in the fight against coronavirus

With the rapidly evolving situation surrounding COVID-19, Tecan is working diligently to provide tools that will help you gain insights into the evolution of the novel coronavirus. 

Our Trio RNA-Seq NGS library prep solution has enabled researchers to successfully study viruses in limited, degraded samples. Four recent, peer reviewed publications have demonstrated the utility of Trio RNA-Seq in detection of novel coronavirus from patient samples as well as providing insight into the SARS-CoV-2 evolutionary history and virulence:

  1. Chen et al. from Wuhan University, China demonstrated the utility of Trio RNA-Seq by sequencing COVID-19 virus genomes from limited patient samples. The genomes of SARS-CoV-2 were successfully analyzed to determine its origin, evolutionary history and virulence.
  2. Shen et al. performed metatranscriptome sequencing for the bronchoalveolar lavage fluid of eight SARS-CoV-2 patients, 25 community-acquired pneumonia (CAP) patients and 20 healthy controls to study viral evolution and how the virus interacts with other microorganisms in the lung . The authors concluded that the virus evolves after infection, which may impact its virulence, infectivity, and transmissibility.
  3. Gong et al. from Research Centre for Emerging Viral Infections, College of Medicine, Chang Gung University, Taiwan successfully identified 12 complete SARS-CoV-2 viral genomes in Taiwan. They demonstrated that the virus showed variations to facilitate adaptation to the environment and various hosts. The researchers concluded that sequencing is a useful tool for tracing infections and monitoring genetic changes in strains in the population. 
  4. Maurano et al. from New York University successfully performed large scale genomic surveillance of 236 patient samples from the NYC metropolitan area. The researchers showed that there was undetected community spread and concluded that the majority of SARS-CoV-2 strains in NYC origniated from Europe. Trio RNA-Seq was chosen over other kits for this study due to a lower rate of duplicate reads, especially for lower viral input samples. 

Our Trio RNA-Seq and Ovation® RNA-Seq System V2 solutions feature Single Primer Isothermal Amplification (SPIA) technology and are well suited for viral detection and monitoring from limiting sample types. SPIA can increase the detection sensitivity to effectively address the challenges of low input and low abundance of pathogens in these samples.

Trio RNA-Seq kit - A Complete NGS workflow with integrated depletion for viral detection

Next generation sequencing (NGS) is a sensitive method that provides detailed sequence based analysis to help address outstanding questions regarding the evolution of the virus, incubation period, at risk population demographics and potential relapse/reinfection of the disease. 

Trio RNA-Seq library preparation kit incorporates our proprietary technologies to enable generation of RNA-Seq libraries from low-input/precious samples while depleting abundant uninformative sequences.

 

Figure 1. The Trio RNA-Seq kit is a complete, streamlined workflow for NGS library construction from challenging and limited samples. 

 

  • Single Primer Isothermal Amplification (SPIA) enabling access to limited and degraded samples as low as 500 pg. SPIA can increase the detection sensitivity to effectively address the challenge of low input and low viral titer, particularly in asymptomatic patients or healthy carriers
  • Enzymatic fragmentation and DimerFree library construction allowing efficient and robust library preparation
  • AnyDeplete depleting abundant uninformative sequences, such as human ribosomal RNA (rRNA), maximizing detection sensitivity without excessive sequencing

The Trio low input RNA-Seq library preparation solution is well suited for pathogen identification and provides additional information on pathogen abundance, viral mutation, spectrum surveillance, and gene expression. This information can be helpful for research studies determining disease incubation time, adequate quarantine period, risks/impact of healthy carriers on the general population and epidemiology, and viral evolution. Trio RNA-Seq with its automation solution is well suited for studies requiring large scale pathogen identification.

 

Researchers from University of New Mexico compared Trio RNA-Seq to their reference Hybrid capture method to determine the underlying cause of respiratory illness from nasalpharyngeal swab samples. The ability of Trio RNA-Seq to detect viruses and other potential pathogens, in this study, is highlighted in Table 1 and Figure 2. Download the full poster on the performance of Trio RNA-Seq kit for viral detection in clinical samples here.

Table 1. RNA was extracted from 12 human nasalpharyngeal swab samples, quantified by Qubit, and processed by both the reference hybrid capture method and the Trio RNA-Seq method. For each sample the RNA concentration as measured by Qubit is shown, along with a virus detected (check) or not detected (empty) by the indicated method. Trio RNA-Seq detected viruses across varying input levels, including cases where the reference method failed.

Figure 2. The hypothesis independent Trio RNA-Seq method offers additional opportunities for discovery. Two samples with no reads mapping to target virus in the reference method were further analyzed for other viral or bacterial species that may cause respiratory symptoms. In Sample A, a significant number of reads mapped to S. pneumoniae, which is a major cause of bacterial pneumonia. Additionally, A. baumannii was found in this sample, which can cause fever, chills, and pneumonia like symptoms. In Sample B, along with A. baumannii, a significant number of reads mapped to Brucella spp., which can cause a variety of symptoms, including vomiting and stomach pains, and O. anthropi, which is an opportunistic pathogen known to cause a variety of symptoms in immunocompromised individuals.

Ovation® RNA-Seq System V2 - Accurate and reproducible amplification of limited input samples

qPCR is a powerful tool that is used for quick, high throughput target validation for determining the presence or absence of pathogens in a sample. Low input amounts and low abundance of the target transcript, such as from nasal swabs, can reduce the effectiveness of this method. 

Based on the proven SPIA technology, our Ovation RNA-Seq System V2  provides global amplification of RNA from limiting samples. The amplification of the sample has a number of benefits including increased detection sensitivity enabling analysis of very low abundance RNA viruses that are below detection levels for standard methods. Our Ovation RNA-Seq System V2 can be effectively integrated with the qPCR workflow to accurately and reproducibly interrogate hundreds of degraded samples, while more of the original precious sample can be archived and stored for later applications such as additional qPCR tests or NGS assays.

 

Figure 3. Ovation RNA-Seq System V2 provides a simple workflow to convert and amplify RNA to micrograms of double-stranded cDNA. The cDNA can be used in a wide range of application such as NGS, qPCR, and sample archiving to obtain the most information from precious, limited samples.

Lab automation solutions for coronavirus research and detection

We provide ready-to-go automation workflows with DreamPrep® solutions for nucleic acid extraction and NGS library prep. DreamPrep NGS workstation combines the Fluent® Automation platform, Infinite® F Nano+ plate reader and our library preparation kits to provide sequencing-ready libraries with unprecedented speed and accuracy. It is a flexible and future-proof library preparation platform for mid/high throughput NGS library preparation and quantification.

The automated workflow for the Trio RNA-Seq Library Preparation Kit on DreamPrep NGS is available now !

Learn more on how DreamPrep solutions can help with coronavirus research.

 

References

  1. Chen, L., et. al. (2020). RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak. Emerging Microbes & Infections, doi: 10.1080/22221751.2020.1725399
  2. Shen Z., et. al. (2020) Genomic diversity of SARS-CoV-2 in Coronavirus Disease 2019 patients. Clinical Infectious Diseases. doi:10.1093/cid/ciaa203
  3. Gong Y., el. al. (2020) Sequence variation among SARS-CoV-2 isolates in Taiwan. bioRvix  doi: 10.1101/2020.03.29.014290
  4. Maurano MT., et. al. (2020) Sequencing identifies multiple, early introductions of SARS-CoV2 to New York City Region. medRxiv doi: 10.1101/2020.04.15.20064931

 

Talk to an Expert

 

For research use only. Not for use in diagnostic procedures