Epidemiological surveillance is conducted to ensure viral diseases match the reference strain and to monitor possible mutations, since any changes in the viral genome can impact public health policies and options, how the illness spreads in the population, potential study of treatment options, and vaccine development research. Thermo Fisher Scientific has a complete solution to assist scientists who are conducting epidemiological studies.
Fast, automated and accurate targeted NGS workflow for SARS-CoV-2 epidemiological investigation
A major challenge for microbiologists and virologists is the prediction of patterns of evolution and emergence of disease agents. RNA viruses like SARS-CoV-2 (the coronavirus responsible for COVID-19) share the biological feature of high genetic variability, which causes them to appear as clouds of mutants. Coronavirus variants also emerge through antigenic shift within animal reservoirs, such as bats, pangolins, and snakes.
Ion Torrent targeted next-generation sequencing (NGS) enables a streamlined research workflow for complete genome sequencing and epidemiological studies of SARS-CoV-2.
The Ion AmpliSeq SARS-CoV-2 Research Panel is designed to cover more than 99% of the SARS-CoV-2 genome, including all potential serotypes, and can be used for complete viral genome sequencing and variant detection. The assay is part of a fast, automated, and accurate targeted NGS workflow that enables coronavirus typing in under a day. This end-to-end solution includes the assay and plug-in suite that was developed in collaboration with researchers at the forefront of the SARS-CoV-2 crisis. Our complementary targeted NGS systems makes SARS-CoV-2 epidemiology research accessible to any lab, regardless of your team’s current level of NGS expertise. Benefits of using Ion Torrent NGS for studying SARS-CoV-2 include:
- Rapid turnaround time
- Highly automated NGS workflow for easier adoption, lower user intervention, and improved lab efficiency
- Accuracy of variants—lower substitution errors for SNVs
- Higher success rates—analyze directly with lower viral loads (as low as 20 copies)
The Ion AmpliSeq SARS CoV-2 Research Panel is now available for the Ion Torrent Genexus Integrated Sequencer. This new NGS solution enables you to rapidly go from nucleic acid to variant report in less than a single day with minimal hands-on time.
Real-time PCR can be used to research viral and human genetic determinants that influence disease susceptibility, spread, and sequelae within a population or large sample size. Real-time PCR testing takes less than 40 minutes, is accurate to <10-copy detection, and has an affordable cost per sample.
Real-time PCR is also an important research tool in the development of future therapeutics and vaccines. As the gold standard for detecting and quantitating gene expression, real-time PCR provides a fast, reliable, and cost-effective means to determine potential responses to drug therapies or study viral loads after administration of treatments or vaccines.
SARS-CoV-2 has shown us that the time to and reproducibility of results are critical in potentially mitigating the impact of a crisis. A rigorous, reproducible workflow built on automation and integrated connectivity produces consistent results with fewer errors, while a coordinated ecosystem gives you complete control and oversight of your research. The following products used in concert with our suite of digital solutions enables you to connect everything: lab automation, data management, and digital partners, to help you move faster when timing is critical.
TaqMan Gene Expression Assays
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For Research Use Only. Not for use in diagnostic procedures.
Viral nucleic acid isolation for SARS-CoV-2 research
Prior to any NGS-based epidemiological study of SARS-CoV-2, researchers need to quickly and efficiently isolate RNA. Features of the MagMAX Viral/Pathogen Nucleic Acid Isolation Kit include:
- Automation-ready protocols designed for Thermo Scientific KingFisher systems
- Flexible protocols accomodate mutiple sample types and input volumes
- Recommended for viral nucleic acid isolation for SARS-CoV-2 to obtain high-quality nucleic acid
For fast, easy, and effective high-throughput sample processing, automate your nucleic acid isolation with the KingFisher Flex system, a versatile benchtop instrument for the processing of 24 or 96 samples per run. Features of this system include:
- Choose from two plate formats for high-throughput purification of 24–96 samples per run
- Easy to install and run (ready to run in 10 minutes or less)
- Choose from two plate formats for wide volume range (20–5,000 µL)
- Download existing protocols from a library, or easily customize protocols using Thermo Scientific BindIt Software
Avoid high levels of contaminating DNA and RNases and maintain a nuclease-free lab with RNaseZap solutions and nuclease-free water, buffers and reagents, and tips and tubes products:
- RNaseZap solution—a room temperature-stable solution for surface decontamination
- Invitrogen Nuclease-Free Water—for nucleic acid isolation, rigorously tested for contaminating nonspecific endonuclease, exonuclease, and RNase activity
- Invitrogen nuclease-free buffers and reagents—commonly used Ambion RNA storage buffers and other buffers and reagents that are rigorously tested for nuclease contamination
- Nuclease-free tips and tubes—a nuclease-free range of plasticware for use in nucleic acid isolation and storage
Collibri Library Prep Kits for Illumina Systems enhance next-generation sequencing (NGS)-based viral surveillance with higher quality sequences and rapid protocols. Full-length genomic coverage can improve the accuracy of monitored transmission patterns and mutation rates of SARS-CoV-2. Unlike transposomic methods, the Collibri DNA Library Prep Kits for Illumina Systems provide full-length, hypothesis-free, genomic coverage using a library prep method that is completed in 1.5 hours. Collibri DNA Library Prep Kits are suitable for genomes of all sizes.
Improve accuracy and speed of RNA sequencing results by adding helper adapters for Illumina NGS directly to RNA. Collibri Stranded RNA Library Prep Kits for Illumina Systems are suitable for host-pathogen studies using the following sequencing methods:
- Whole-transcriptome sequencing
- mRNA sequencing
- Total RNA sequencing
Study differences in gene expression that may offer insight into why some people respond differently to SARS-CoV-2 infection. Collibri 3’ mRNA Library Prep Kits for Illumina Systems require as few as 2–5 M reads, reducing the cost of sequencing to generate gene expression profiles by as much as 90%. Simple, rapid informatics and low-cost sequencing permit higher numbers of samples to be analyzed quickly for greater experimental power.
Invitrogen SuperScript reverse transcriptases were developed for improved thermostability, processivity, and cDNA yields to enable superior performance with even the most challenging RNA samples. With over 50,000 citations, reviews, and publications, SuperScript reverse transcriptases are the superior choice for vaccine development.
Did you know our latest technology, SuperScript IV, allows researchers to perform cDNA synthesis in only 10 minutes?
See what other researchers are saying at www.thermofisher.com/ssiv
For Research Use Only. Not for use in diagnostic procedures.