Mutation Surveillance

Mutation Surveillance: Study the Plasticity and Epidemiology of Infections

In addition to increasing the throughput of assays, Next Generation Sequencing (NGS) can be used to study the viral genome1,2,3,4. Subtle mutations in the viral genome can be informative to study sources of infection5. Additionally, this technology allows studying host risk factors that predispose to infections6,7 and broadly screen for co-infections with other pathogens8. The workflows used for mutation surveillance are overall very similar to virus detection, but different kits for library preparations and downstream analysis may be used9.

SARS-CoV-2突变分析

随着在行业内发现的SARS-CoV-2突变越来越多,人们对病毒测序的需求也不断增加。快速发现新的突变体可以让我们能够及早评估其毒性、传染性和耐药性。Eppendorf为这一工作流程中的每个步骤都提供了仪器和耗材方案。联系我们 了解详细信息。您是否在寻找自动化的工作流程解决方案?请查看此处

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 will enable 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 secure, 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

  • Essential 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 μl volume, a thermo-stable frame and perfect fit with 96-well magnets

More about Consumables


Tempering and Mixing

  • ThermoMixers are essential 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 Mastercycler


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 sequencing can take place, it is recommended to check the quality and concentration of the libraries. 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 low handling 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 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 for loading pooled libraries to the flow cells safely.

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 samplesMore about Sample storage solutions

1 Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding
R. Lu, X. Zhao, J. Li, et al. Lancet, 2020
10.1016/S0140-6736(20)30251-8

2 A Novel Coronavirus from Patients with Pneumonia in China, 2019
N. Zhu, D. Zhang, W. Wang, et al., New England Journal of Medicine, 2020
www.nejm.org/doi/full/10.1056/NEJMoa2001017

3 A rapid, low cost, and highly sensitive SARS-CoV-2 diagnostic based on whole genome sequencing
BG St Hilaire, NC Durand, N Mitra et al.
doi.org/10.1101/2020.04.25.061499
bioRxiv Posted May 11, 2020

4 A pneumonia outbreak associated with a new coronavirus of probable bat origin
P. Zhou, XL Yang, XG Wang, et al., Nature, 2020

5 Introductions and early spread of SARS-CoV-2 in the New York City area
AS. Fonzalez Reiche, MM Hernandez, M Sullivan, et al., 2020
doi.org/10.1101/2020.04.08.20056929
Medrxiv posted on April 16,2020

6 Illumina, UK Agencies Partner on £28M Sequencing Study of COVID-19 Patients
May 12, 2020 staff reporter GenomeWeb
www.genomeweb.com/sequencing/illumina-uk-agencies-partner-28m-sequencing-study-covid-19-patients

7 CDC Leads Public-Private Consortium to Coordinate SARS-CoV-2 Genome Sequencing in US
May 01, 2020 staff reporter GenomeWeb
www.genomeweb.com/sequencing/cdc-leads-public-private-consortium-coordinate-sars-cov-2-genome-sequencing-us

8 Capturing sequence diversity in metagenomes with comprehensive and scalable probe design
HC Metsky, KJ Sidde, A Gladden-Young et al., Nature Biotechnology 2019

9 CDCgov / SARS-CoV-2_Sequencing:
A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.
CDC, 2020
Accessed May 25, 2020
github.com/CDCgov/SARS-CoV-2_Sequencing