Virus Detection NGS
Scientist working with pipetting robot for nucleic acid purification and NGS

Virus Detection: Nucleic Acid Purification and Next Generation Sequencing

Due to a shortage in RT-qPCR kit supplies, there have been limited SARS-CoV-2 screening capacity to trace the spread of the virus. To keep the virus in check without a vaccine, simulations suggest that 80% of the population would have to undergo screening every 10 days1-which equals 23 million tests per day in the United States2. To meet this type of demand, it has been argued that significant upscaling could be performed if RT-qPCR were substituted by Next-Generation Sequencing (NGS)3.

The methods and equipment shown are intended for molecular research applications. They are not intended, verified, or validated for use in the diagnosis of a disease or other human health conditions.

Collect Samples

Primary samples can be swabs, blood or other body fluids.

Storage and Management  

  • Samples can be stored in high quality Cryo tubes
  • An Ultra-Low Temperature Freezer allows long term storage of primary samples
  • The eLabJournal® and eLABInventory allow for effortless archiving and documentation 

Eppendorf CryoCube F570 ULT freezer for storage of lab samples More about Sample storage solutions

Aliquot Samples

To process the collected samples, samples need to be transferred to tubes or plates.

Manual Liquid Handling

  • Mechanical or Electronic Single Channel Pipettes are ideal for precise reformatting of samples from primary vessels
  • Filter Tips assure the sample integrity of primary samples

More about Manual Liquid Handling


Automated Liquid Handling

  •  Benchtop Pipetting Robots support you to deal with an increased sample throughput

More about Automation Solutions


Plates and Tubes

  • Leachable free plates and tubes for optimal processing and storage of aliquoted samples

More about Laboratory Consumables


Storage and Management

  • Samples can be stored using high-quality Cryo tubes
  • Ultra-Low Temp Freezer allows long term storage of aliquoted samples
  • eLabJournal® and eLABInventory allow painless archiving and documentation

Eppendorf CryoCube F570 ULT freezer for storage of lab samples More about Sample storage solutions

Nucleic Acid Extraction

Nucleic Acid Extraction (also known as Nucleic Acid Purification) refers to the isolation of viral DNA or RNA used with magnetic-bead or filter/silica-based protocols.

Manual Liquid Handling

  • Single Channel Pipettes are ideal for processing in tube format. Multichannel pipettes are optimal for processing in plate format.
  • Filter Tips assure the sample integrity when handling primary samples
  • A Dispenser and Combitips® help add reagents in a quick and precise way. They also help minimize handling steps, used materials and reduce the risk of cross-contamination.

More about Manual Liquid Handling


Automated Liquid Handling

  • Benchtop Pipetting Robots allow walk-away automation of Magnetic-Bead-Based and Filter-Based Extraction Kits

More about Automation Solutions


Plates and Tubes

  • Leachable free plates and tubes for optimal results
  • A wide range of consumables allow you to pick the best-suited consumable for your protocol, ranging from single tubes to deep well plates
  • Safe and fast processing: easy one-hand handling, perfect fit on magnets, centrifugation and heat safe, automation-friendly

More about Laboratory Consumables


Tempering and Mixing

  • ThermoMixers are especially helpful for lysis steps, but also allow to help with other incubation steps, like resuspension and neutralization
  • Suited for magnetic bead homogenization
  • Easily fits the biosafety cabinet
  • Interchangeable blocks make it easy to process and clean plates and tubes

More about Temperature Control and Mixing


Centrifugation

  • Key for processing filter-based protocols, especially single spin columns
  • A wide variety of centrifuges and adapters allow you to handle plates and single vessels of each size and format

More about Centrifugation


Storage and Management

  • Extracted nucleic acids can be stored in an Ultra-Low Temperature Freezer
  • eLabJournal® and eLABInventory allow painless archiving and documentation

Eppendorf CryoCube F570 ULT freezer for storage of lab samples More about Sample storage solutions

NGS library preparation

Viral genomic material needs to be processed to generate libraries ready for Next-Generation sequencing. These libraries are mostly generated with commercially available reagent kits. The kit protocols involve a multi-step process that includes several magnetic bead cleanup steps, as well as multiplex PCR.

Manual Liquid Handling

  • Single Channel Pipettes are ideal for processing samples in tube format. Multichannel Pipettes are optimal for processing in plate format
  • Superior precision for highest reproducibility and handling low volumes
  • A perfectly fitted tip for your pipette helps you to maximize precision
  • Filter Tips drastically reduce the risk of cross-contamination
  • A Dispenser and Combitips® help add reagents in a quick and precise way. They also help minimize handling steps, used materials and reduce the risk of cross-contamination.

More about Manual Liquid Handling


Automated Liquid Handling

  • Benchtop pipetting robots allow the automation of whole NGS library preparation protocols or single critical steps

More about Automation Solutions


Plates and Tubes

  • Leachable free plates and tubes avoid interference with the NGS sequencing
  • Semi skirted twin.tec® plates are ideally suited for NGS library preparation; as the combine up to 300 uL volume, a thermo-stable frame and perfect fit with 96-well magnets

More about Consumables


Tempering and Mixing

  • ThermoMixers are important for all heat incubation steps
  • Suited for magnetic bead homogenization
  • Interchangeable blocks make it easy to process both plates and tubes

More about Temperature Control and Mixing


Amplification

  • Mastercycler® X50 offers high cycling speed and outstanding block homogeneity
  • Ideally suited for demanding PCR applications like Multiplex PCR and critical heat incubation steps

More about Amplification


Centrifugation

  • Crucial to avoid air bubbles that interfere with the reactions, and to spin down samples and reagents
  • A wide variety of centrifuges and adapters allow you to handle plates and single vessels of each size and format

More about Centrifugation

Library Quality Control (QC), Normalization and Pooling

Before the actual sequencing can take place, it is recommended that the quality and concentration of the libraries are checked. Some protocols also require a concentration normalization of the libraries. Pooling is usually the last step before the libraries are sequenced.

Manual Liquid Handling

  • Single Channel Pipettes are ideal for precise qPCR set-up for QC, library distribution for normalization, and pooling before sequencing.
  • Superior precision for highest reproducibility and handling low volumes
  • A perfectly fitted tip for your pipette helps you to maximize precision
  • Filter Tips drastically reduce the risk of cross-contamination
  • A Dispenser and Combitips help add reagents and diluent in a fast and precise way, which allows you to speed up both QC and normalization

More about Manual Liquid Handling


Automated Liquid Handling

  • Benchtop Pipetting Robots can support library QC and take over tedious normalization routines

More about Automation Solutions


Plates and Tubes

  • Leachable free plates and tubes reduce interference with the fluorescent signal of qPCR reaction for QC
  • White plates help achieve maximum signal strength
  • The ultra-clear film is perfect to seal plates

More about Consumables


Centrifugation

  • Crucial to avoid air bubbles that interfere with the fluorescent signal, and to spin down samples and reagents
  • A wide variety of centrifuges and adapters allow you to work with plates and single vessels of any size and/or format
  • Concentrators can deal with low library concentrations

More about Centrifugation


Storage and Management

  • Libraries can be stored in an Ultra-Low Temperature Freezer if they are not sequenced directly
  • eLabJournal® and eLABInventory allow painless archiving and documentation

Eppendorf CryoCube F570 ULT freezer for storage of lab samples More about Sample storage solutions

Sequencing and Data Analysis

The actual NGS run can detect and quantify viruses, viral subspecies, or viral genes. For further analysis, samples can be stored after sequencing for follow-up experiments.

Manual Liquid Handling

  • Single Channel Pipettes are ideal to securely load pooled libraries to the flow cells.

More about Manual Liquid Handling

 


Storage and Management

  • Plates and tubes can be stored using Ultra-Low Temperature Freezer
  • The eLabJournal® and eLABInventory allow for effortless archiving and documentation

Eppendorf CryoCube F570 ULT freezer for storage of lab samples More about Sample storage solutions

1 Population-scale testing can suppress the spread of COVID-19
J Taipale, P Romer
medRxiv posted May 1, 2020

2 Is Population-Scale Testing for SARS-CoV-2 Feasible?
Adam Bonislawski
360Dx Posted May 22,2020

3 How to Deploy Millions of COVID-19 Tests Per Day
Whitepaper Ginko Bioworks, 2020
www.ginkgobioworks.com/2020/05/04/how-to-deploy-millions-of-covid-19-tests-per-day/
Published May 4,2020