Introduction

QuantSeq-Pool Targeted SARS-CoV-2 Panel for Illumina®

  • The most economical solution for true mass screening
  • Flexible solution starting from 768 – 36,864 samples per Next Generation Sequencing (NGS) run and extendable to millions of samples
  • Scalable to population size
  • Get results within 24 hours
  • High specificity for SARS-CoV-2 (99.8 %)
  • Based on Lexogen’s industry-leading QuantSeq and QuantSeq-Pool NGS technologies
  • Save significant amounts of consumables (plastic ware and tips) compared to other NGS-based approaches

“Thanks to an initiative on the Vienna Biocenter Campus, our company is screening each employee every three days. This allows us to identify (and quarantine) infected individuals early enough to stop the spread of the virus. At this frequency, so far none of our infected employees have contaminated their colleagues. This actually helped us to finish the rapid development of this mass test.” Stéphane Barges, Chief Executive Officer, Lexogen GmbH

“Testing infected people regularly after infection, could allow them to return to work as soon as possible with confidence when they are not infectious anymore. This would save a tremendous amount of labor days and avoid a temporary closing of companies or of some activities.” Alexander Seitz, Chief Innovation Officer and Founder, Lexogen GmbH

Official Press Release in English
Offizielle Pressemitteilung in deutscher Sprache

Mass screening

The impact of the Coronavirus pandemic has called for a new, more efficient screening approach to identify and isolate infected individuals. Current testing methods are limited in their throughput and do not allow for the scale of screening required to test repeatedly at population scale. Lexogen has therefore developed the QuantSeq-Pool Targeted SARS-CoV-2 Panel, a targeted RNA sequencing kit that leverages the ultra-high throughput capacity of NGS. Early sample barcoding allows to trace individual samples throughout the workflow while triple indexing enables the analysis of millions of samples in parallel. This way, the panel allows to quickly identify and isolate infected individuals even if they are asymptomatic. These individuals are then quarantined before they are infectious, thereby stopping the spread of the disease (Figure 1).

Lexogen_SARS-CoV-2_Infographic_01_1500px

Figure 1 | Mass testing can stop the spread of COVID-19 by identifying infected persons before the onset of symptoms.

Results in 24 hours

This new COVID test works with RNA extracted not only from nasopharyngeal but also from conveniently obtained gargle samples, making the procedure painless and allowing for self-sampling. Lexogen offers the SARS-CoV-2 Rapid RNA Extraction Kit for extraction of 96 samples in 15 minutes with full automation suitability for high-throughput processing (Figure 2).

Lexogen_SARS-CoV-2_Infographic_03

Figure 2 | Convenient gargle-based self-sampling as the initial step in a mass-screening workflow for the detection of SARS-CoV-2 infections. Lexogen’s SARS panel enables the analysis of thousands of samples per laboratory within 24 hours.

Comparison of COVID-19 test methods

Lexogen Panel
(NGS, RNA-Seq)
PCR
(RT-qPCR)
LAMP
(RT-LAMP)
Antigen
(Ag)
Benefit
Target Viral RNA Viral RNA Viral RNA Viral antigen
Method Targeted conversion of RNA to DNA, library preparation and ultra high-throughput sequencing, bioinformatic data evaluation. Targeted conversion of RNA to DNA and amplification of DNA which is visualised on a real-time fluorescence measurement. Conversion of RNA to DNA and amplification of DNA which is visualised by a color change in the reaction tubes. Antibody binds to a protein on the surface of the virus and is visualised on a lateral flow strip.
Sputum sampling
(gargling)
yes_icon yes_icon yes_icon no
  • Sputum sampling by gargling is non-invasive and painless
  • Can be conducted anywhere (at home or at work)
  • No trained personnel with protective equipment needed
Nasal sampling (nasopharyngeal) yes_icon yes_icon yes_icon yes_icon
  • Nasal (nasopharyngeal) samples have higher virus load and increase sensitivity of the assay but they can be very painful and require trained personnel with protective equipment
Testing at Point of Care (PoC) no no no yes_icon
  • Testing at PoC is fast and yields results immediately
  • Performing and evaluating the test at diagnostic (Dx) labs allows for certified workflows
Testing site and trained personnel required for sampling No No / Yes No / Yes Yes
  • De-centralised sampling at home and work reduces risk of infection at testing site and removes many logistical challenges
Max number of samples per run 36,864 96 96 1
  • High multiplexing is necessary for ultra high-throughput
Pooling of individual molecular-barcoded samples of samples w/o retaining identity of samples w/o retaining identity N/A
  • Early molecular barcoding allows batch processing of samples while retaining their identity
Sensitivity for samples with
Ct ≤ 30
> 99% 100% 97.50% 84% – 97.6%
  • high sensitivity = few false negatives
  • low sensitivity = some infected individuals are not detected
Specificity 99.80% 98% – 100% 99.70% > 97%
  • high specificity = few false positives
  • low specificity = non-infected potentially diagnosed as positive
Suitable for symptomatic individuals yes_icon yes_icon yes_icon yes_icon
  • Identification of individuals with high viral load and symptoms
Suitable for asymptomatic individuals (screening) yes_icon yes_icon yes_icon no
  • Identification of individuals with low viral load and without symptoms
Lab / Assay time 16 h 2 h 2 h 15 min
Sample-to-result time 20 h 5 h – 2 days 6 h 15 min
  • Time to result is important in PoC settings
  • Mass screening setups benefit from results in 24 h
Cost per sample < € 12 € 40 – € 60 € 9 – € 12 € 7.10 – € 13
Additional technical costs no RNA extraction RNA extraction no
Total cost per sample < € 15 > € 110 > € 15 > € 20
Further costs sample transport sample transport sample transport Testing sites to be set up and sampling done by trained personnel with protective equipment

Recommendations for companies and institutions

To reduce the economic and social impact of the pandemic we suggest the following approach for every public and private company as well as for public institutions (especially schools and healthcare institutions):

  • Perform a regular testing of all employees (to avoid leakage) every three days to identify and quarantine infected individuals early enough to avoid infection of K1 (contact cases).
  • Perform a daily testing of infected people (after 4 or 5 days) to assess their level of infectivity and get them back to work as soon as they are no more infectious.

What are the consequences of these preventive measures?

  • It becomes unnecessary to quarantine all close contact persons.
  • Infected people who are not infectious anymore could be back to work before the end of the current long quarantine period without endangering their colleagues.

What are the benefits of these preventive measures?

  • Reduce the death toll and number of infected.
  • Create a safe working environment that also reduces the stress for the employees (as per our experience).
  • Maintain schools, hospitals, and elderly homes open while providing a safe workspace and more serenity for all the stakeholders (pupils, parents, teachers, patients, healthcare workers, etc.).
  • Avoid a lockdown and keep the economic activities up and running to ensure a continuous revenue stream for the companies and the country.
  • Reduce the dramatic pandemic negative impact on the EBIT of companies and GDP of countries.

Downloads

QuantSeq-Pool SARS-CoV-2 Product Flyer

pdf QuantSeq-Pool SARS-CoV-2 Product Flyer – release 23.11.2020

COVID-19 Mass Screening Info Flyer

pdf COVID-19 Mass Screening Info Flyer – in English – release 23.11.2020
pdf COVID-19 Mass Screening Info Flyer – auf Deutsch – release 23.11.2020

COVID-19 Mass Screening Info Flyer for companies

pdf COVID-19 Mass Screening Info Flyer for companies – in English – release 23.11.2020
pdf COVID-19 Mass Screening Info Flyer for companies – auf Deutsch – release 23.11.2020

Lexogen Comparison of COVID-19 test methods

pdf Lexogen Comparison of COVID-19 test methods – release 23.11.2020