Epidemiological research

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.

Virus typing

Identifying the types and subtypes of viruses is essential to good disease control. A wide variety of research methods can be used to differentiate virus variants of which molecular techniques are used most frequently. By sequencing a specific variable region of the viral genome, one can investigate whether selected isolates of a certain species are phylogenetically related. 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. Advanced molecular technologies like next-generation sequencing (NGS) enables complete SARS-CoV-2 genome sequencing, including all variants and potential serotypes.

Viral typing with Ion Torrent NGS

Fast, automated and accurate targeted NGS workflow for SARS-CoV-2 epidemiological investigation

Targeted NGS is a rapid and accurate solution for viral genomes from a variety of epidemiological samples from viral investigations. Our viral typing NGS solutions provide ultra-high sensitivity, scalability, and rapid turnaround time, which are all vital to viral monitoring and investigation research. 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 variantslower 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.

Learn more about our portfolio of Ion Torrent NGS instrumentation for SAR-CoV-2 research or request project costs.

Customer spotlight

Triche_Timothy_06-18-10

Dr. Timothy J. Triche, MD, PhD

Co-Director of Center for Personalized Medicine at Children’s Hospital Los Angeles

Webinar: SARS-CoV-2 Research: Implications of Viral Sequencing

View on demand ›

De novo sequencing using Ion Torrent NGS

In addition to targeted sequencing, which covers >99% of the viral genome and variants, Ion Torrent systems can be used for hypothesis-free (de novo) genome sequencing of SARS-CoV-2 by NGS.

Product Cat no.
Ion AmpliSeq SARS-CoV-2 Research Panel Contact your sales representative
  1. Italian Researchers Identify New SARS-CoV-2 Gene Variants that Provide Clues to Coronavirus Epidemiology
  2. Molecular characterization of SARS-CoV-2 from the first case of COVID-19 in Italy - M.R. Capobianchi et al – National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
  3. High-density amplicon sequencing identifies community 1 spread and ongoing evolution of 2 SARS-CoV-2 in the Southern United States - Ryan P. McNamara et al - The University of North Carolina at Chapel Hill School of Medicine, Department of Microbiology and Immunology
  4.  Phylogenetic pattern of SARS-CoV-2 from COVID-19 patients from Bosnia and Herzegovina: lessons learned to optimize future molecular and epidemiological approaches - Teufik Goletic et al - Veterinary faculty of University of Sarajevo, Zmaja od Bosne 90, 71000 Sarajevo, Bosnia and Herzegovina

Variant confirmation with Sanger sequencing

While NGS analyses can be used for complete viral genome sequencing and variant detection of the SARS-CoV-2 genome, Sanger sequencing is still considered the gold standard sequencing method for verifying the sequence of specific genes, including those already sequenced through Ilumina NGS due to its high degree of accuracy.  It is being used to sequence and confirm variants of different SARS-CoV-2 genes within clusters of symptomatic and asymptomatic individuals (1-4).

The entire workflow can be completed, from sample to answer, in less than one workday.  We offer products to support the entire workflow from PCR amplification to data analysis.  The SeqStudio genetic analyzer is an affordable, low-throughput cartridge-based benchtop genetic analyzer that eliminates complex instrument set-up to deliver Sanger sequencing runs in as little as 30 minutes. 

Learn more about Sanger sequencing solutions for SARS-CoV-2 research ›

  1.  Yuan, Y,. et al. (2020) “Molecular Epidemiology of SARS-CoV-2 Clusters Caused by Asymptomatic Cases in Anhui Province, China” Research Square preprint (https://dx.doi.org/10.21203/rs.3.rs-29833/v1)
  2.  Holland, LA., et al. (2020) “An 81 nucleotide deletion in SARS-1 CoV-2 ORF7a identified from sentinel surveillance in Arizona (Jan-Mar 2020)” J. Virology (https://doi.org/10.1128/jvi.00711-20)
  3.  Liu, Z., et al. (2020) “Identification of common deletions in 1 the spike protein of SARS-CoV-2”. J. Virology (https:// doi:10.1128/JVI.00790-20)
  4.  Tabibzadeh, A., et al. (2020) “SARS-CoV-2 Molecular and Phylogenetic analysis in COVID-19 patients: A preliminary report from Iran” Infection, Genetics and Evolution (https://doi.org/10.1016/j.meegid.2020.104387)


Virus monitoring

Accurate understanding and monitoring of the SARS-CoV-2 virus is essential for effective response. Monitoring is important to help public health decision makers know where the disease is, how quickly it is spreading, and to longitudinally monitor the effectiveness of public health measures on outbreak containment or mitigation. Monitoring also plays a role in understanding cross-species transmission of the virus and its spatial spread over evolutionary time and at human-wildlife interfaces. We offer several cost-effective molecular tools for SARS-CoV-2 disease monitoring research, from technologies like real-time PCR and Sanger sequencing for specific genes/targets to whole genome sequencing to capture all variants using NGS.

Targeted NGS workflow for SARS-CoV-2

Targeted NGS is a rapid and accurate solution for viral genomes, suitable for monitoring SARS-CoV-2 infection and spread, including zoonotic transmission. Publications have shown Ion Torrent NGS to be useful with a variety of challenging sample types, including animal models, swabs, FFPE, and waste water.

Ion Torrent targeted NGS solutions provide ultra-high sensitivity, scalability, and rapid turnaround time, which are all vital to viral monitoring and investigation research. It 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 Ion Targeted NGS features rapid, highly automated workflow that yields accurate SARS CoV 2 genome sequencing from challenging samples.

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.

Learn more about our portfolio of Ion Torrent NGS instrumentation for SAR-CoV-2 research or request project costs.

  1. Presence and vitality of SARS-CoV-2 virus in wastewaters and rivers - Sara Giordana Rimoldi et al - Laboratorio di Microbiologia Clinica, Virologia e Diagnostica delle Bioemergenze, ASST Fatebenefratelli Sacco, Milan, Italy;
  2. Lam, T.T., Jia, N., Zhang, Y. et al. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature 583, 282–285 (2020). https://doi.org/10.1038/s41586-020-2169-0
  3. Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases - Miroslav Sekulic et al - Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH; Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH


SARS-CoV-2 monitoring using real-time PCR

Real-time PCR can be used to research viral and human genetic determinants that influence the distribution and patterns of disease conditions 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.

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

Catalog # Assay ID Name Size
4331182 Vi06439674_s1 CoV_HKU1 250 rxns
4331182 Vi06439673_s1 CoV_NL63 250 rxns
4331182 Vi06439671_s1 CoV_229E 250 rxns
4331182 Vi06439644_s1 MERS_CoV 250 rxns
4331182 Vi06439634_s1 SARS_CoV 250 rxns

To order, search the Assay ID or Name using our ordering tool.    Ordering tool

Other products


SARS-CoV-2 monitoring with Sanger sequencing and fragment analysis by capillary electrophoresis

Sanger sequencing is a simple, fast, and cost-effective orthogonal gold-standard method to monitor SARS-CoV-2 identified by NGS or by RT-PCR.  The entire workflow can be completed, from sample to answer, in less than one workday. It is being used by several labs globally to confirm the identity of SARS-CoV-2 in wastewater samples. It is also being used to confirm the origin and cross-species transmission of different coronaviruses, which is important in understanding potential sources of zoonotic transmission (1-3).

Blog post: SARS-CoV-2 in Wastewater: A Potential Early-Warning Method

Fragment analysis by capillary electrophoresis (CE) provides an attractive method for  rapid testing of multiple targets. Multiplexed qPCR solutions detect small numbers of pathogens. The relatively small capacity of multiplexed qPCR reactions can limit throughput when large numbers of targets or pathogens need to be detected. Fragment analysis gives researchers another tool for analyzing the presence of genomic sequences of pathogenic organisms using a method that is rapid, simple, and sensitive.

 Protocol: Detection of RNA from SARS-CoV-2 using fragment analysis ›
Application Note: Multiplex target fragment analysis for detection of viral pathogens including SARS-CoV-2 ›

Fragment analysis by CE can be used to identify microbial signatures associated with different disease phenotypes. It relies on amplification of 16S-23S rRNA interspace (IS) regions in bacteria to produce PCR fragments that vary in length and frequency depending upon bacterial species. Each PCR fragment can be separated and detected on a genetic analyzer. The resulting fragment patterns are compared to a curated database to determine the species present in the sample.

Blog post: Could Differences in Microbiota Explain Variability in SARS-CoV-2 Susceptibility?
Learn more about Sanger sequencing and fragment analysis solutions for SARS-CoV-2 research ›

  1. Valitutto, M.T., et al. (2020) “Detection of novel coronaviruses in bats in Myanmar,” PLoS One 15(4): e0230802.( https://doi.org/10.1371/journal.pone.0230802)
  2. Latinne A., et al. (2020) Origin and cross-species transmission of bat coronaviruses in China. (bioRxiv preprint doi: https://doi.org/10.1101/2020.05.31.116061)
  3. Huong, N.Q., et al (2020) “Coronavirus testing indicates transmission risk increases along 2 wildlife supply chains for human consumption in Viet Nam, 2013-2014 (bioRxiv preprint doi: https://doi.org/10.1101/2020.06.05.098590.)


Sample Prep

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 accommodate multiple 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 Purification systems, 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:

Next-generation sequencing—library preparation for Illumina systems

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.

Gene synthesis

Product Cat no.
GeneArt Gene Synthesis and Gene-to-Protein Services See thermofisher.com/geneart

cDNA synthesis for epidemiological research

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