The SARS-CoV-2 crisis underscores the urgency of understanding virus origins, transmission, and societal health effects. Next-generation sequencing (NGS) has shown significant utility in the fight against infectious diseases, including those caused by Ebola, Zika, H1N1 influenza, and, most recently, SARS-CoV-2. Since March 2020, NGS has proved invaluable in rapid, scalable studies on coronavirus epidemiology, including transmission rate1 and viral evolution, contributing to over 214,076 samples sequenced as of November 2020.2 NGS has also led to greater understanding of the basic biology of SARS-CoV-2, specifying how the virus affects its hosts, and why infection responses range from asymptomatic to severe symptoms, influencing societal and economic impact. In concert with phylogenetic information, characterizing host genetics and immune responses through NGS directly supports vaccine and therapeutic development research, as well as broader investigations of great interest to public health.
Together, the Ion GeneStudio™ S5 system, associated assays, and software analysis tools from Thermo Fisher Scientific comprise a complete targeted NGS workflow solution that enables the speed and accessibility demanded by infectious disease research. The Ion GeneStudio S5 system’s scalability allows for application flexibility and has been used to address various facets of SARS-CoV-2 research. A list of applications appears in Table 1.
The Ion GeneStudio S5 system utilizes massively parallel sequencing to enable rapid and scalable sequencing. Assays run on the Ion GeneStudio S5 system leverage Ion AmpliSeq™ technology based on multiplex PCR, a common method used to detect coronavirus and monitor viral infections. Highly multiplexed PCR helps identify and target tens to hundreds of genes across mutation types, including SNPs, indels, fusions, and copy number variants. This Ion Torrent™ NGS platform is scalable, with diverse throughput capabilities suited to SARS-CoV-2 research, including strain discovery, immune repertoire and microbiome studies, transcriptome analysis, and more, all on a single instrument. Turnaround time for the complete NGS workflow for infectious disease research from nucleic acid to report is rapid, with sequence data available in as little as 24 hours.
The Ion GeneStudio S5 sequencer, in conjunction with Ion AmpliSeq technology, enables automation with end-to-end workflows that minimize human intervention errors with greater accessibility, thus improving both workflow and overall laboratory efficiencies. Its accuracy in detecting single-nucleotide variants (SNVs), and sensitivity down to viral loads as low as 20 copies, instill confidence in NGS results, from nucleic acid to data, in less than 24 hours with about 45 minutes of hands-on time (Figure 1).
Ion Torrent targeted NGS technology translates chemically encoded genetic information into digital information on a semiconductor chip. The result is simpler, faster, more scalable, cost-effective sequencing. Five Ion Chip options are available to enable a sequencing throughput range of 2 million to 130 million reads.3
The power of the Ion GeneStudio S5 Series is evident from its versatility in answering complex questions on existing or emerging diseases, such as research into cancer, inherited disorders, gene expression analysis, reproductive health, and, of particular interest today, infectious diseases.
Ion GeneStudio S5 works with a wide range of NGS assay kits covering a wide spectrum of infectious disease and pathogen studies. Specifically among these is the Ion AmpliSeq™ SARS-CoV-2 Research Panel for epidemiological investigations. This panel consists of two pools, with amplicons 125–275 bp in length covering >99% of the coronavirus genome, including variants, with a turnaround time of about 24 hours and approximately 45 minutes of hands-on time. This instrument-software-assay solution works with sample RNA loads as low as 1 ng. Key applications using the Ion GeneStudio S5 system and Ion AmpliSeq SARS-CoV-2 Research Panel include contact tracing, wastewater monitoring, and population surveillance to track viral spread and evolution, and more.4 Additionally, the system's sequencing capabilities are notably suited to viral variant detection to support future vaccine development research and maximize vaccine efficacy.
Very strong data have emerged on the association of host response to microbiome profiles.5 The human gut microbiome (HGM) is a critical component of the immune response to viral infection, but its workings are poorly understood. Alterations to the relative populations of gut microbes involved in antiviral immunity can guide both vaccine efficacy and our understanding of disease susceptibility. When used with the Ion GeneStudio S5 system, the Ion AmpliSeq™ Microbiome Health Research Kit provides comprehensive, cost-effective profiling of the HGM, which includes fully integrated data analysis useful for biomarker identification and characterization.6
Similarly, the Oncomine™ Immune Response Research Assay is a targeted NGS gene expression assay that measures low-expressing genes involved in inflammatory signaling. Generally, the Oncomine™ T-cell receptor (TCR) and B-cell receptor (BCR) assays are used to investigate host response to viral infection, to identify disease severity biomarkers, perform targeted immune profiling, to characterize T and B cells to predict immune-related adverse events, and predict patient's response to future therapies. In addition, the Ion GeneStudio S5 System has enabled greater understanding of the immunologic profiles of patients with severe SARS-CoV-2 infection7 with:
The ongoing SARS-CoV-2 crisis presents an unprecedented imperative for humankind to understand a previously unknown virus, its evolution and spread, and its effects on human health. Solving the coronavirus puzzle will entail research in obvious areas already recognized: genetics, epidemiology, virology, and population health, as well as future, longer-term health issues that may arise later in life as a consequence of infection.
The Ion GeneStudio S5 system has thus far been a valuable tool, empowering researchers to address concerns about coronavirus and its effects on human health. Together with targeted assay kits, the Ion GeneStudio S5 system’s flexibility and scalability supports investigations into every aspect of the coronavirus infection cycle and specific cellular responses. With an easy-to-use suite of software tools, researchers can quickly go from sample to answer, regardless of bioinformatics expertise.
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1. Publication: Epidemiology of COVID-19 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7364648/
2. The GISAID Initiative https://www.gisaid.org/
3. Brochure: Ion GeneStudio S5 Series Systems https://assets.thermofisher.com/TFS-Assets/CSD/brochures/ion-genestudio-s5-ngs-system-brochure.pdf
4. White paper: SARS-CoV-2 Research Applications Using the Ion GeneStudio S5 System https://assets.thermofisher.com/TFS-Assets/CSD/Reference-Materials/whitepaper-targetedNGS-sars-cov-2-genestudio.pdf
5. Poster:A Targeted Next Generation Sequencing Assy to Analyze and Characterize the Gut Microbiome for Health Research http://assets.thermofisher.com/TFS-Assets/BID/posters/targeted-ngs-assay-analyze-characterize-microbiome-health-research-poster.pdf
6. Ion AmpliSeq Microbiome Health Research Kit, Ion 540 Bundle https://www.thermofisher.com/order/catalog/product/A46496?SID=srch-srp-A46496#/A46496?SID=srch-srp-A46496
7. Publication: Two Distinct Immunopathological Profiles in Autopsy Lungs of COVID-19 https://www.nature.com/articles/s41467-020-18854-2
For Research Use Only. Not for use in diagnostic procedures.