IAB SARS-Cov2

IAB SARS-Cov2

The IAB company offers the optimized “All-in-one IAB SARS-Cov2 workflow” – from sample to data – for application of Next-Generation-Sequencing (NGS) techniques for monitoring of the SARS-CoV-2 genome via two different hybridization-capture solutions coupled with validated de novo assembly approaches.

We offer two options: 

  1. Sequencing the coronavirus genome using Twist SARS-CoV-2 Research Panel Kit (Twist Bioscience), which targets particularly the novel coronavirus genome.
  2. Sequencing the coronavirus together with other viruses using Respiratory Virus Oligo panel (Illumina), that targets next to the SARS-CoV-2  a whole set of ~30 common respiratory viruses.  

In both hybridization-capture methods, ds cDNA from the original RNA is synthesized by the  NEBNext (New England Biolabs) kit. No matter which solution you prefer, both approaches can generate data for high-quality genome assembly.

More information you can find in our study in which we present two methodological solutions and our experience with them (Performance of targeted library preparation solutions for SARS-CoV-2 whole-genome analysis, Klempt et al. 2020, Multidisciplinary Digital Publishing Institute)

Our validated de novo assembly pipeline is prepared for your data and tested on both hybridization-capture solutions presented above. This “All-in-one IAB SARS-CoV2 workflow” provided high quality, de novo assembled sequences of SARS-CoV-2 that you can rely on. (Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020,  Alm et al.  2020, Eurosurveillance report)

  • Sample anonymization
  • Sample QC
  • Synthesis of ds cDNA
  • Library preparation and library QC
  • Illumina sequencing
  • Output quality control and filtering
  • De novo assembly and data analysis 
  • Results sharing 

Sample requirement

  • Total RNA (or a mixture of DNA and RNA) isolates, no Mg2+, EDTA/EGTA, guanidium, etc.
  • RNA concentration: ≥ 10 ng/µl (lower concentration possible after consultation)  
  • ΔCt= up to 24 (recommended, see study)
  • Minimum sample volume: 15 µl

Kits for library preparation

  • Illumina DNA prep for Enrichment coupled with Respiratory Virus Oligo panel (Illumina)

or

  • NEBNext Ultra II Directional RNA Library Prep Kit for Illumina coupled with Twist SARS-CoV-2 Research Panel Kit (Twist BioScience)

Sequencing

    • MiSeq – NovaSeq (Illumina)
    • Pair-end sequencing 2×150 bp
    • Internal standard – PhiX Spike-in

 

  • BaseSpace Sequencing Hub for data storage and sharing 

 

Data QC

  • Recommended read depth: depending on the application and sample Ct 

(starting at 0,5M PE reads) 

Bioinformatic analysis 

  • Advanced data QC
  • De novo assembly (preferred) in alternation to reference mapping

Delivery time

  • 8 weeks since sample delivery to the data output
  • accelerated service on request iabio@iabio.eu

Certification

  • ČSN EN ISO 9001:2016
  • ČSN EN ISO 13485 ed.2:2016