research

Understanding disease progression and associated biomarkers is key to developing treatments for novel viruses. Even though patients may have varying immune responses, it’s possible to determine widespread prevention and treatment options. Thermo Fisher Scientific offers a complete portfolio of tools and technologies to enable SARS-CoV-2 virus research, supporting collaboration and the acceleration of lifesaving discoveries.

Pathogen biology

SARS-CoV-2, the virus responsible for COVID-19, is an enveloped, non-segmented, single-stranded positive-sense RNA (+ssRNA) virus and a newly identified β-coronavirus. The genome of ~30 kb consists of multiple open reading frames (ORFs) encoding four structural proteins: Spike (S), Envelope (E), Membrane (M), and Nucleocapsid (N), and a variety of non-structural proteins.

The SARS-CoV-2 viral lifecycle has yet to be resolved, a critical step to studying infection progression. Even though the replicative lifecycle of viruses differs greatly between species and categories, there are common stages that are essential for viral replication: attachment, entry and uncoating, replication, assembly, and release.

Untangling the viral replication pathways from host cell functions is challenging because viruses hijack cell machinery upon infection, creating cell conditions more conducive for virus production. Thermo Fisher Scientific offers an array of technologies and products to elucidate the basic stages of the viral life cycle and aid in the investigation of the biology of SARS-CoV-2. Some of these technologies and products are highlighted in the following sections.

Understand variation in the SARS-CoV 2 genome and how that information can be used to track community spread.

  AmpliTaq Gold DNA Polymerase Platinum II Taq Hot-Start DNA Polymerase
Compatible with TaqMan probes Yes Yes
Cycling time 60 sec/kb  15 sec/kb 
PCR sensitivity   ++ +++
Universal annealing temperature   No Yes

Cloning of viral genes

To learn more about isolation of viral RNA for SARS-CoV-2 research, visit the Sample Prep section on the Epidemiological Research page.

Nucleic acid quantification and qualification for SARS-CoV-2

By absorbance

  • Quantify DNA, RNA, and protein in seconds using only 1–2 µL of sample—no need for dilution. Thermo Scientific NanoDrop One instruments are built with Thermo Scientific Acclaro Sample Intelligence technology to help you determine if your sample is suitable for downstream applications.
  • Prevent costly delays—Acclaro software identifies contaminants (protein, phenol, guanidine salts) and provides corrected concentrations to ensure experimental success
  • Quickly collect data—save time with Auto-Blank and Auto-Measure modes
  • Troubleshoot results in real-time—information alerts trigger guided technical support for fast answers

By fluorescence

The Invitrogen Qubit Fluorometer is designed to quickly and specifically quantify DNA or RNA.

  • Qubit assay dyes bind selectively to DNA, RNA, or protein, making it orders of magnitude more sensitive than UV absorbance
  • Uses as little as 1 μL of sample, even with very dilute samples
  • Fast, reliable detection of degraded RNA with the Invitrogen Qubit RNA IQ Assay

Compare nucleic acid quantitation and qualification technologies ›

Sample integrity is essential to the success of every storage approach.  So is the ability to easily share information designed to accelerate lifesaving discoveries.  Thermo Fisher Scientific offers the most diverse, cutting-edge portfolio of storage solutions and services designed to help you do both.  Our biobanking sample collection, preparation and automation equipment, cost storage solutions, wireless monitoring, tubes, vials, containers, reagents, and biobanking services give you the power to secure and preserve your samples, track your inventory, streamline productivity, and meet your toughest laboratory challenges.  At the same time, our informatics solutions enable you to share insights and information critical to advancing science and discovering the next big idea.

Lab equipment—reliable sample protection and preparation solutions with exceptional contamination protection, control and a wide range of options to fit your needs
BioBanking solutions—transforming life science research
Clinical research consumables—providing high quality and reliability to protect your samples and your staff
Gibco Viral Transport Medium Kit— to enable the safe transport and storage of samples for viral testing; suitable for the transport of specimens suspected to contain virus
RNase inhibitors—prevent degradation of RNA viruses by naturally-abundant RNases

For viruses to access intracellular sites of replication in the cytosol or nucleus, cellular membranes present the first barrier for entry into the host cell. Viral-encoded envelope or capsid proteins serve as binding partners for host cell molecules or receptors, and their binding specificity defines the cell and tissue tropism, infectivity, and thus the nature of disease. Traditional plaque assays are being replaced by neutralization assays, such as the plaque reduction neutralization test (PRNT) to test antibodies that neutralize and prevent virions from infecting cultured cells. PRNT is now required by the Centers for Disease Control (CDC) for some viruses utilizing high-content screening instrumentation to measure viral infectivity and neutralization (1).

Product Cat. No.
CellInsight CX5 Platform Request a quote ›
CellInsight CX7 Platform Request a quote ›
CellInsight CX7 LZR Platform Request a quote ›

Learn more about Invitrogen high-content screening platforms ›

Receptor recognition by SARS-CoV-2

The entry of coronaviruses into target host cells has been shown to be facilitated by the Spike (S) protein, with the SARS-CoV-2 S1 subunit of the spike protein critical for binding to the cell surface receptor angiotensin-converting enzyme 2 (ACE2). Priming of the S protein by the cellular serine protease, TMPRSS2, generates the S2 subunit required for fusion of the viral and cellular membrane, facilitating entry of the virus into the host cell (2).

 

Tracking internalization

The entry mechanism of coronaviruses has been shown to be mediated via the endocytic pathway. The exact mechanism of endocytosis has yet to be determined, with reports indicating both clathrin-dependent and –independent endocytosis (3). Typically, internalized viruses are directed through the endosomes to the lysosome. Viral uncoating is a highly variable process that occurs at different stages after viral entry and may be influenced by pH, lipid composition, proteolytic cleavage, and redox reactions among other factors (4).

Thermo Fisher Scientific offers an extensive portfolio of Invitrogen cell imaging products and technologies to help researchers track the internalization of SARS-CoV-2 viral particle.

Invitrogen probes for imaging cell structure

Viral spike proteins reside on the surface of viruses and are used to bind to host cells, enabling viral infection. Knowledge of the precise, 3D structure of these proteins is essential for the generation of specific, effective drugs and vaccines. It also provides general insight into how the virus evades the immune system.

Virus-host cell interaction

In order for a virus to be effective, it needs to hijack the host cell and replicate. Therefore, the interaction of the virus with host cell proteins is a crucial part of this strategy. This interaction not only ensures the replication of the virus, but it is also a strategy for the virus to evade the defense mechanisms initiated by the host cells. Examining the virus-host cell protein interactions can provide insights into processes such as viral entry, virus genome replication within the host cell, and the ways the viral genome can spread across the cell. Additionally, examining virus-host cell protein interactions could yield valuable information and help scientists develop broadly acting antiviral therapeutics. A number of mass spectrometry techniques have been used for many years to study protein structure and protein-protein interactions and can be applied to study virus-host cell interactions.

Learn more ›

Virus research with cryo-EM—providing high resolution data on antibody-antigen interaction
Cryo-TEM structure of the SARS-CoV-2 spike in the prefusion confirmation
Thermo Scientific Glacios Cryo-TEM
Thermo Scientific Orbitrap Eclipse Tribrid Mass Spectrometer

References

  1. Gates I, Olson V, Smith S, Patel N, Damon I, Karem K. Development of a High-Content Orthopoxvirus Infectivity and Neutralization Assays. PLoS One. 2015;10(10):e0138836.
  2. Hoffmann M, Kleine-Weber H, Schroeder S, et al. SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell. 2020;181(2):271‐280.e8.
  3. Yang N, Shen HM. Targeting the Endocytic Pathway and Autophagy Process as a Novel Therapeutic Strategy in COVID-19. Int J Biol Sci. 2020;16(10):1724‐1731.
  4. Yamauchi Y, Helenius A. Virus entry at a glance. J Cell Sci. 2013;126(Pt 6):1289‐1295.


TaqMan Gene Expression Assays

Catalog # Assay ID Name Size
4331182 Vi06439674_s1 CoV_HKU1 250 rxns
4331182 Vi06439646_s1 CoV_OC43 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
4331182 Hs01085333_m1  Human ACE2 250 rxns
4331182 Hs01122322_m1  Human TMPRSS2 250 rxns
4331182 Hs00947439_m1 Human CTSB 250 rxns
4331182 Hs00964650_m1  Human CTSL 250 rxns
4331182 Hs00174265_m1  Human ANPEP 250 rxns
4331182 Hs00897386_m1 Human DPP4 250 rxns
4331182 Hs00949382_m1  Human ST6GAL1 250 rxns
4331182 Hs00920870_m1  Human ST3GAL4 250 rxns

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

The uncoating and release of viral RNA into the cytosol results in the translation of viral proteins from the six or more open reading frames (ORFs) identified in coronaviruses. Translation begins at ORF1 a/b, which encodes a large polyprotein that is cleaved to generate at least 16 nonstructural proteins (nsps) that are involved in viral replication (1,2). These nsps include replicases that are involved in generating additional full-length genomes (1). The remaining ORFs encode for four structural proteins: Spike (S), Envelope (E), Membrane (M), and Nucleocapsid (N), and several accessory proteins (1).

One approach to detection of SARS-CoV-2 RNA is performed through branched DNA (bDNA) signal amplification technology. The presence of viral RNA transcripts in infection models can be confirmed through bDNA technology in imaging or flow cytometry using the Invitrogen ViewRNA Assay or Invitrogen PrimeFlow RNA Assay, respectively. These assays for SARS-CoV-2 provide the following advantages:

  • RNA measured directly in the sample source
  • Viral transcript identification at the single cell level with high signal-to-noise ratio
  • Determination of transcript copy number and subcellular localization
  • Simultaneous detection of multiple RNA targets in combination with immunophenotyping

For RNA viral studies that require reverse transcription (RT), researchers can rely on SuperScript IV, our newest RT enzyme. Reliability and performance of SuperScript IV Reverse Transcriptase products help facilitate:

  • Superior sensitivity to detect RNA input amounts down to 0.01 pg total RNA
  • 10 minute RT reaction time for fast performance
  • Significantly better resistance to contaminating inhibitors

See how the enzyme was used in a SARS-CoV-2 research study:
Xie X, Muruato A, Lokugamage KG, et al. (2020) An Infectious cDNA Clone of SARS-CoV-2.Cell Host Microbe S1931-3128(20)30231-6.

References:
1. Perlman S, Netland J. Coronaviruses post-SARS: update on replication and pathogenesis. Nat Rev Microbiol. 2009;7(6):439‐450.
2. Kumar S., Nyodu R., Maurya V.K., Saxena S.K. (2020) Morphology, Genome Organization, Replication, and Pathogenesis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). In: Saxena S. (eds) Coronavirus Disease 2019 (COVID-19). Medical Virology: From Pathogenesis to Disease Control. Springer, Singapore

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

The assembly of the coronavirus particle starts with the helical nucleocapsids, which are formed by the interaction of newly synthesized viral genomic RNA with the nucleocapsid phosphoproteins (1). The triple-spanning membrane glycoprotein M is translated on membrane-bound polysomes and co-translationally inserted into the membrane of the endoplasmic reticulum (ER) and transported to the ER-Golgi intermediary compartment (ERGIC). At the ERGIC, the helical nucleocapsid interacts with the C-terminal domain of the M protein, which is exposed to the cytosol (2). In a process thought to be mainly driven by its transmembrane domain, M oligomerization leads to the formation of lattice structures into which the S and E membrane proteins are integrated (1,2). The structure is then transported by secretory vesicles to the plasma and released. The final coronavirus particle consists of the helical nucleocapsid surrounded by a lipid layer consisting of inserted spike (S), membrane (M), and envelope (E) proteins (2).

Expi293 Expression System for structural biology applications—a suite of products that enables the study of viral surface proteins by providing high titers of uniformly glycosylated proteins, the ability to modulate expression levels of proteins, and protein labeling kits for streamlined studies by X-ray crystallography or Cryo-EM

References:
1. Tseng YT, Wang SM, Huang KJ, Lee AI, Chiang CC, Wang CT. Self-assembly of severe acute respiratory syndrome coronavirus membrane protein. J Biol Chem. 2010;285(17):12862‐12872. 
2. Siu YL, Teoh KT, Lo J, et al. The M, E, and N structural proteins of the severe acute respiratory syndrome coronavirus are required for efficient assembly, trafficking, and release of virus-like particles.J Virol. 2008;82(22):11318‐11330. 

The structure of the virus has a profound effect on its interaction with host cells and how it functions during its lifecycle. In general, viruses are composed of RNA or DNA surrounded by a capsid composed of proteins and glycoproteins. The capsid can vary depending upon the virus, but its primary goal is to protect the viral genome. Some viruses are further encompassed by membrane envelopes composed of lipids and proteins. The surface of the envelope has additional proteins, specifically glycoproteins, which are involved in the process of binding to the host cells for viral entry. A number of mass spectrometry tools are available for the characterization of the different parts of the SARS-CoV-2 virus.

Learn more ›

  • Glycoproteomics
  • Glycomics
  • Native MS
  • HDX-MS

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Host response

The host response to SARS-CoV-2 infection, from host pathogen interactions and signaling events to innate and adaptive mediated immune responses, plays a critical role in studies of human health implications. Currently, treatment of SARS-CoV-2 infection is palliative, with the primary cause of mortality being respiratory failure from acute respiratory distress syndrome (ARDS) (1).  Recent studies show that management of the immune-mediated inflammatory cytokine response may be beneficial. In severe infection this response is often referred to as cytokine release storm or syndrome (CRS), which can lead to hyper-inflammation, multi-organ failure, and eventually death (1). Due to the wide range of symptoms there is research evidence that the immune response factors vary greatly among subjects, providing some with stronger early defenses that never progress to severe cases. It is therefore critical to understand the cellular and biochemical differences in the innate and adaptive immune response in patients that are asymptomatic, have mild symptoms, or have severe CRS (2,3).

From large scale genomics and proteomics to more targeted approaches, Thermo Fisher Scientific offers researchers an extensive portfolio of solutions for immunological and infectious disease studies.

References:

  1. Mehta P, McAuley DF, Brown M, et al. COVID-19: consider cytokine storm syndromes and immunosuppression. Lancet. 2020;395(10229):1033‐1034.
  2. Huang C, Wang Y, Li X, et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China [published correction appears in Lancet. 2020 Jan 30;:]. Lancet. 2020;395(10223):497‐506.
  3. Wang D, Hu B, Hu C, et al. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China [published online ahead of print, 2020 Feb 7]. JAMA. 2020;323(11):1061‐1069.

Maintaining the integrity of your samples at every point from collection to storage is imperative to obtaining quality sample and associated data. This begins with the preparation of biological samples, which lays the groundwork for a range of critical research objectives such as drug discovery, disease research and beyond. Our solutions support sample preparation, from extraction to fractionation and aliquoting, while maintaining traceability from the point of collection at a range of throughput levels for biobanks at any scale. The safety and security of your samples is non-negotiable. We understand the dual importance of sample integrity and inventory management and offer a comprehensive sample storage solution designed to protect your samples, track your inventory, and provide peace of mind.

The identification of molecular markers or molecular signatures of biological processes using high throughput technologies capable of comprehensive analysis of genomic and other biological molecules has provided significant insights and helped with understanding of host response to infection and disease progression.

Hypothesis-free target identification and evaluation of host gene expression is achieved with higher accuracy, in less time, using Invitrogen Collibri Library Prep Kits for Illumina systems.

  • Increase the quality of sequences to obtain the entire genome
  • Improve accuracy and speed of RNA sequencing results by adding adapters for Illumina NGS directly to RNA
  • Identify differences in gene expression that may offer insight into why some people become gravely ill and others do not show symptoms

Complete SARS-CoV-2 genome sequencing with Ion Torrent NGS

Ion Torrent targeted next-generation sequencing (NGS) enables a streamlined research workflow for complete genome sequencing and epidemiological studies of SARS-CoV-2. Through the use of a set of highly specific, universal coronavirus primers in combination with a high-fidelity master mix, all genomic segments are amplified and the DNA amplicons are sequenced on any Ion Torrent system to deliver highly accurate coronavirus typing in under a day. The Ion AmpliSeq SARS-CoV-2 Research Panel is compatible with the Ion GeneStudio S5 and Ion Torrent Genexus systems.  In addition to the Ion AmpliSeq SARS-CoV-2 Research Panel workflow, which covers >99% of the viral genome and variants, Ion Torrent GeneStudio systems can be used for de novo (whole genome) sequencing of SARS-CoV-2 .

Sanger sequencing to confirm partial and full genome SARS-CoV-2 sequence following NGS

Sanger sequencing is a simple, fast, and cost-effective orthogonal method to confirm SARS-CoV-2 identified by NGS or by RT-PCR.  It was used in the connection of viral contigs to generate the first full length genome sequence of the novel coronavirus SARS-CoV-2.

The entire workflow can be completed, from sample to answer, in less than one workday.  Thermo Fisher Scientific offers 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 setup to deliver Sanger sequencing runs in as little as 30 minutes. 

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

Understand how genomic variation can impact response to pathogens

Learn more about T-cell and B-cell receptor variation, as well as how gut microbiome can influence immune response to SARS-CoV-2.

Understand variation in the SARS-CoV 2 genome and how that information can be used to track community spread.

Learn more about the Ion AmpliSeq SARS-CoV-2 Reseach Panel or request project costs ›

While clinical guidance issued by the CDC currently lists laboratory markers that are associated with increased COVID-19 illness severity, including but not limited to elevated liver enzymes, lymphopenia, and neutropenia (1), there is an immediate need by researchers to identify and develop other biomarkers to understand the biology of the host response to the infection. These include biomarkers to monitor cellular response, including the innate sensing of viral infections, host susceptibility factors, the activation of anti-viral pathways, and induction of pro-inflammatory responses, to help characterize the molecular networks underlying symptomatic infections and the progression and pathogenesis of the infections.

2D and 3D cell culture model for biomarker research

Researchers rely upon 2D cell culture models that are easy to use and well-established for studying infectious diseases. Thermo Fisher Scientific provides cell culture products for basic research to specialty assays. These include cell culture media, high activity growth factors, fetal bovine serum, and tissue culture grade plastics for imaging or various cell attachment needs.

Cardiovascular, pulmonary, hematological, and neurological complications in the context of SARS-CoV-2 infection emphasize the importance of establishing relevant physiological models to understand underlying cellular mechanisms. 3D cellular models like organoids and spheroids offer an opportunity to better understand complex biology and have shown great potential in recent publications (1,2). Explore end-to-end solutions with Thermo Fisher 3D cell culturing products.

Contact cell model services about your project today ›

Discover tools, protocols and product solutions to produce your 3D model, including the Nunclon Sphera 3D culture system ›

Cellular analysis using imaging and western blotting

In order to study pathways and biomarkers in 2D or 3D cellular models in the context of SARS-CoV-2 infection, commonly used techniques such as imaging and western blotting can provide spatiotemporal and quantitative analysis of protein expression. For example, Lamers et al. studied 3D airway and gut organoids in the context of SARS-CoV-2 infection to understand the general viral response utilizing Thermo Fisher imaging reagents for mounting specimens, performing nuclear and cytoskeletal staining, and antibody based detection for specific biomarkers (1).

To detect biomarkers in cell or tissue lysates, Thermo Fisher Scientific provides end to end western blotting solutions, or use this convenient blot builder tool to help determine the correct western workflow products to fit your experimental needs.

Gene expression analysis to identify biomarkers for infection severity

Recent publications have shown host response to pathogen infection to be as important as viral strain sequence differences in understanding human health implications of SARS-CoV-2 infection The Ion AmpliSeq Transcriptome Human Gene Expression Kit and Ion AmpliSeq Transcriptome Mouse Gene Expression Kit are comprehensive tools for gene-level expression analysis. Targeting >20,000 human or mouse RefSeq transcripts in a single reaction with an FFPE-compatible workflow, the complete Ion AmpliSeq Transcriptome solution is compatible with existing downstream microarray or next-generation sequencing (NGS) analysis pipelines for fast and straightforward data interpretation.

QuantiGene Plex assays provide a fast and high-throughput solution for multiplexed gene expression quantitation, allowing the simultaneous measurement of up to 80 genes of interest in a single well of a 96- or 384-well plate. The QuantiGene Plex assay is hybridization-based and incorporates branched DNA (bDNA) technology, which uses signal amplification rather than target amplification for direct measurement of RNA or DNA transcripts. The assay is extremely easy to use with a simple ELISA-like workflow, and does not require RNA purification. It works with difficult sample types including degraded and cross-linked RNA in FFPE tissues and directly with blood, with no RNA purification required.

Product Cat No.
QuantiGene assays Request a quote ›
QuantiGene Singleplex Request a quote ›
QuantiGene Plex Request a quote ›
Ion GeneStudio S5 System Request a quote ›

 

Immune response and microbiome biomarker identification

Understanding of the immune repertoire through T-cell and B-cell receptor sequencing in addition to gut microbiome profiles can identify important biomarkers for understanding response to SARS-CoV-2.

References:
1. Lamers MM, Beumer J, van der Vaart J, et al. SARS-CoV-2 productively infects human gut enterocytes [published online ahead of print, 2020 May 1]. Science. 2020;eabc1669.
2. Yang L, Han Y, Nilsson-Payant BE, et al. A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids. Cell Stem Cell. 2020;27(1):125-136.e7.

Multi-dimensional host response research with Ion Torrent Next-Generation Sequencing (NGS)

Recent publications have shown host response to pathogen infection to be as important as viral strain sequence differences in understanding human health implications of SARS-CoV-2 infection. Deeper understanding of the adaptive immune system, inflammation markers, and the human microbiome powers better insights into its role in health and response to pathogens, leading to crucial developments in future treatments such as immunotherapies. The Ion Torrent SARS-CoV-2 research portfolio enables a multi-dimensional research approach to repertoire sequencing and immune response, in addition to end to end workflows for broader transcriptome sequencing or human microbiome analysis. Each targeted next-generation sequencing (NGS) assay is powered by the accuracy and sensitivity of Ion Torrent technology to help discover more from precious samples along with highly automated end to end workflows including robust informatics tools. Combining host response with epidemiological studies, the Ion Torrent SARS-Cov-2 research portfolio presents a rapid and scalable way to address multiple facets of infectious disease research.

For human research studies:

For mouse studies:

The Ion GeneStudio S5 System is a scalable, targeted-NGS workhorse with wide research application breadth and throughput capability and is compatible with our complete portfolio of immune response assays.

Learn more about the Ion GeneStudio S5 System or request a quote ›

QuantiGene gene expression assays for biomarker verification

The Invitrogen QuantiGene Plex assays provide an accurate and precise method for single or multiplexed targeted biomarker gene expression quantitation. The QuantiGene assay is also available as a single plex assay, for the measurement of one gene target per well, while the QuantiGene Plex assay is used for multiplexed gene expression quantitation and can be used to measure up to 80 gene targets per well.

  • Direct from sample quantitation: no RNA purification
  • Precisely detect subtle changes (smaller than 10%)
  • Standardized platform with simple workflow (96- and 384-well)
Product Cat No.
QuantiGene Singleplex Request a quote ›
QuantiGene Plex Request a quote ›

The host’s immune system is its defense system against viral infections. The characterization of the various molecules involved in the immune systems response to viruses is necessary for the development of treatments that can be used to suppress viral replication and propagation, as well as alleviate any symptoms of diseases caused by the virus. Mass spectrometry characterization and quantitation of proteins and metabolites can provide important information about how the immune system functions.

Learn more ›

  • Bottom-up proteomics
  • Quantitative proteomics
  • Posttranslational modifications
  • Metabolomics

Flow cytometry analysis of intracellular and cell-surface targets can help elucidate a more complete mechanism of the immune response to viral infections. Cossarizza et al. demonstrated guidelines to safely analyze samples for intracellular cytokine detection and relative differences among immune cells (1). Important cytokine targets, such as those listed in the table below, as well as cytotoxic markers Granzyme A, B, K and M, Perforin, and Granulysin, can be analyzed using Invitrogen flow cytometry antibodies with the Invitrogen Attune NxT flow cytometer to understand the immune response during SARS-CoV-2 infection (1,2). The targets listed below can also be analyzed using immunoassays found in the following section.

Target Distribution Function
IFNgamma Cytotoxic T cells, NK cells
Viral and parasitic responses
TNFalpha
Macrophages
Viral and parasitic responses, regulation of immune cells
IL-6
Activated T cells
Viral responses
IL-10
Macrophages, Th2 cells
Enhances antibody production, anti-inflammatory cytokine
IL-17
Th17 cells
Pro-inflammatory cytokine
Granzyme A
Cytotoxic T cells, NK cells
Target cell apoptotic lysis, cell-mediated immune responses
Granzyme B
Cytotoxic T cells, NK cells
Target cell apoptotic lysis, cell-mediated immune responses
Granzyme K
Cytotoxic T cells, NK cells
Target cell apoptotic lysis, cell-mediated immune responses
Granzyme M
Cytotoxic T cells, NK cells
Target cell apoptotic lysis, cell-mediated immune responses
Granulyisn
Cytotoxic T cells, NK cells
Target cell apoptotic lysis, cell-mediated immune responses
Perforin
Cytotoxic T cells
Viral response, pore forming
PD-1
Activated T cells
Immune inhibitory molecule
Tim-3
Th1, Th17, Tregs, CD8+ T cell subsets
Immune inhibitory molecule

In addition, Invitrogen offers out-of-the-box solutions such as the essential phenotyping kits, which are efficient and cost-effective methods for flow cytometry-based analysis. These ready-to-use kits have been designed for the reliable identification of T-cell subsets including CD4+, CD8+, regulatory T-cells (Tregs), and T helper cell subsets in human blood on any flow cytometer equipped with violet 405 nm, blue 488 nm, and red 633 nm lasers, such as the Invitrogen Attune NxT flow cytometer. If you need a larger custom panel to discover more about your leukocyte lineages, request a quote below or build your own panel using the Invitrogen Flow Cytometry Panel Builder.

Find antibodies for flow cytometry ›

References:
1. Cossarizza A, Gibellini L, De Biasi S, et al. Handling and Processing of Blood Specimens from Patients with COVID-19 for Safe Studies on Cell Phenotype and Cytokine Storm [published online ahead of print, 2020 Apr 10]. Cytometry A. 2020;10.1002/cyto.a.24009.
2. Thevarajan I, Nguyen THO, Koutsakos M, et al. Breadth of concomitant immune responses prior to patient recovery: a case report of non-severe COVID-19. Nat Med. 2020;26(4):453‐455.

Immunological assays can help pinpoint cellular subsets and associated secreted molecules important for viral infection and host immunology. They are used to understand virulence and attenuation and to develop neutralizing vaccines.

Invitrogen immunoassay kits are easy to use for quantification of inflammatory-related cytokines and chemokines in serum, plasma, or other biological fluids.

 

ELISA for single analyte detection

Immunoassay plates are available with a variety of surfaces optimized to capture the biomolecule of your choice. To help identify the best surface for your application see our  immunoassay plate guide.

Measure key inflammatory cytokines and chemokines such as IFNγ, IL-1B, IL-2, IL-6, GM-CSF, IP-10, MCP-1, MIP-1a, and TNFα or acute phase indicators such as Ferritin or CRP.

See the complete list of ELISA menu selection.

 

Serological assays

Serological blood assays can detect antibodies that remain in the blood after SARS-CoV-2 infection. This can enable determination of convalescent plasma samples, or those that contain SARS-CoV-2 specific antibodies. Search for anti-human IgG or IgM, or plate reader-based detection below:

Find anti-human antibodies for use in serological testing (lateral flow or ELISA) ›
See plate reader instrumentation for fluorescence and luminescence readouts with ELISA, serological assays ›

Advanced qPCR-based immunoassay for fast, high-sensitivity detection

ProQuantum high-sensitivity immunoassays enable detection of inflammatory markers in only two hours. No wash steps minimize contaminated waste. Run on any qPCR instrument, the assay provides a large dynamic range to easily measure low and elevated protein levels while only consuming 2 µL of serum sample.

Learn more and see the complete list of ProQuantum targets available ›

ProcartaPlex multiplexed immunoassays

ProcartaPlex multiplex immunoassays use the Luminex xMAP (multianalyte profiling) technology that enables the simultaneous detection and quantitation of up to 65 protein targets in a single 25–50 µL sample of plasma, serum, cell culture supernatants, or other bodily fluids. In the case of SARS-CoV-2 infection, ProcartaPlex immunoassays provide customizable panels to study Cytokine Release Storm (21 preselected targets commonly found in literature), or use our pre-configured panels for your viral research.

Recombinant proteins

Our recombinant proteins are low-endotoxin and validated via bioassay and SDS-PAGE. They are provided in a carrier-free format ideal for cell culture or production of standards for ELISA or western blotting.

Find your protein of interest ›

Thermo Scientific Orbitrap Eclipse Tribrid Mass Spectrometer Learn more ›
Thermo Scientific Orbitrap Fusion Lumos Tribrid Mass Spectrometer Learn more ›
Thermo Scientific Orbitrap Exploris 480 Mass Spectrometer Learn more ›
Thermo Scientificb Orbitrap Exploris 240 Mass Spectrometer Learn more ›

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Translational research

The translational and pre-clinical research communities have responded quickly to SARS-CoV-2 outbreak by undertaking a variety of approaches to block viral infection and treat pathogenesis. Understanding disease mechanisms and the associated biomarkers through relevant experimental models, advanced cell engineering and protein modification techniques has expanded research capabilities. Thermo Fisher Scientific is committed to providing reliable and easy-to-use solutions, services and support to help meet the demanding needs of clinical and translational research, enabling researchers to transition rapidly from discovery research to translational settings and into the development of treatments

Experimental models: expression systems and cell-based assays

Recombinant viruses provide excellent tools for the introduction of genetic material into a variety of host cells. We offer a wide range of tools including purification kits, plasmids, packaging systems and transduction kits and appropriate host cell lines for viral expression. In addition, we also offer tools for in vitro protein expression (also known as in vitro translation, cell-free protein expression, cell-free translation, or cell-free protein synthesis). Although in vitro expression is not practical for commercial large-scale recombinant protein production, it has a variety of features that make it considerably more useful and flexible for many research applications.

Invitrogen GeneArt Subcloning and Plasmid Services Learn more ›
Gibco Expi Protein Expression Systems Learn more ›
Cell Free Protein Expression Systems Learn more ›
Gibco LV-MAX Lentiviral Production system Learn more ›

 

Quantigene

Product Cat No.
QuantiGene assays Learn more ›
QuantiGene Singleplex Request a quote ›
QuantiGene Plex Request a quote ›

 

TaqMan Probe-based chemistry – For Research Use Only. Not for use in diagnostic procedures.

Catalog# Assay ID Name
4331182 Hs01085333_m1 / SARS-CoV-2 ACE2
4331182 Hs01122322_m1 / SARS-CoV-2 TMPRSS2
4331182 Hs00947439_m1 / SARS-CoV-2 CTSB
4331182 Hs00964650_m1 / SARS-CoV-2 CTSL
4331182 Hs00174265_m1 / HCoV-229E ANPEP
4331182 Hs00897386_m1 / MERS-CoV DPP4
4331182 Hs00949382_m1 / Influenza ST6GAL1
4331182 Hs00920870_m1 / Influenza ST3GAL4

Genome editing

To help you understand how the genome influences phenotype, our complete toolset offers trusted solutions for every step in the cell engineering workflow. Our collection of optimized, validated technology systems are designed to work together to eliminate the trial-and-error phase and help you get answers faster and with less effort.

Discover the genome editing tool ›

Easily create accurate and more successful knock-in experiments with TrueDesign Genome Editor. Our free design tool has an intuitive point-and-type interface that provides unrivaled flexibility and support for creating genome edits

 

CRISPR-mediated gene editing confirmation with Sanger sequencing

Because the repair process is not completely efficient or accurate in genome editing experiments, Sanger sequencing can be used to determine the efficiency of CRISPR-mediated genome editing in primary transformed cell cultures, and to determine successful editing events in secondary clones.

Applied Biosystems genetic analysis instruments and reagents provide:

  • Easy and unambiguous identification of single nucleotide polymorphisms (SNPs), sequence deletions, and insertions produced in a cellular population during gene editing
  • Minor Variant Finder Software and the cloud-based Sanger Variant Analysis module to determine the frequency of SNPs; compatible with Tracking of Indels by Decomposition (TIDE) software—a widely available tool for analyzing the efficiency of genome editing events

Learn about the genetic analysis tools available to confirm your gene editing experiments ›

 

GeneArt gene synthesis and services

Synthesis and protein engineeringGeneArt Gene Synthesis is a cost-effective method for obtaining customized DNA constructs that are 100% sequence accurate, allowing you to free up time and resources.

High-Q Strings DNA Fragmentsan economical and time-saving alternative to PCR that maintains the GeneArt Gene Synthesis benefits of flexibility, superior performance, and exceptional accuracy. GeneArt Strings and GeneArt High-Q Strings DNA fragments are compatible with any downstream cloning method.

GeneArt Gibson Assembly Cloning kitsGeneArt Gibson Assembly enables the construction of large and seamless constructs and in conjunction with GeneArt Gene and DNA fragment synthesis, allowing for fast and accurate construction of target Plasmid vectors.

 

DNA sequence amplification

Platinum SuperFi II DNA Polymerase—With >300x fidelity of Taq DNA polymerase and efficient amplification of DNA up to 40 kb, Platinum SuperFi II DNA Polymerase offers exceptional sequence accuracy and long-range amplification for cloning and mutagenesis of viral sequences.

 

Clone confirmation by Sanger sequencing

One of the most common applications of Sanger sequencing is the analysis of inserts subcloned into plasmids. Applied Biosystems BigDye chemistries are widely used for Sanger sequencing and are an integral part of plasmid sequencing workflows. The SeqStudio Genetic Analyzer has several features that offer benefits to researchers performing basic plasmid sequencing methods. The instrument is preloaded with sequencing modules optimized for short (<300 bp), medium (500 bp), and long (>600 bp) read lengths, and can also be customized on the instrument to meet specific needs. The cloud-based Sanger Quality Check application provides an intuitive set of tools to analyze sequencing traces.

Transfection reagents and instruments

A broad range of Invitrogen transfection reagents and electroporation solutions optimized for efficiency, viability, and reproducibility and designed for effective delivery of nucleic acids. These include the Lipofectamine family of transfection reagents and the Neon electroporator.

Clone confirmation by Sanger sequencing

One of the most common applications of Sanger sequencing is the analysis of inserts subcloned into plasmids. Applied Biosystems BigDye chemistries are widely used for Sanger sequencing and are an integral part of plasmid sequencing workflows. The SeqStudio Genetic Analyzer has several features that offer benefits to researchers performing basic plasmid sequencing methods. The instrument is preloaded with sequencing modules optimized for short (<300 bp), medium (500 bp), and long (>600 bp) read lengths, and can also be customized on the instrument to meet specific needs. The cloud-based Sanger Quality Check application provides an intuitive set of tools to analyze sequencing traces.

GeneArt Gene-to-Protein Service

GeneArt Genes-to-Protein Service is a fast and efficient way to obtain correctly folded, native protein from transiently transfected mammalian cells. Starting with only the nucleotide sequence, we can provide purified protein within a few weeks. We clone your expression-optimized gene into one of our expression vectors, produce transfection-grade plasmid DNA, and then use one of our advanced expression systems to obtain high expression yields to support research needed for rapid protein production.

Protein purification

Easily extract, purify, clean up, and concentrate your proteins of interest with our kits, reagents, and devices. These products are optimized for a wide range of tissue and cell types and are compatible with a broad range of protein purification resins and formats, which offer more choices and better protein recovery. Desalt, buffer exchange, remove contaminants, and concentrate proteins with our secure and efficient devices and resins.

Crosslinking and labeling tools

We offer a wide range of products for the crosslinking, biotinylation, pegylation, and fluorescent labeling of proteins, antibodies, and peptides. Use our crosslinking or biotinylation reagent selection tool to find the optimal reagent for your application, or access our helpful technical handbook to help improve your bioconjugation results.

Antibody labeling

We offer a range of antibody labeling kits to choose from. Direct labeling of your primary antibody does provide two key advantages:

  • Multiple primary antibodies of the same isotype or derived from the same species can easily be used in the same experiment.
  • Primary antibodies directly labeled with a fluorophore often produces lower background fluorescence and less nonspecific binding than labeled secondary antibodies.

Historically, researchers have relied upon 2D cell culture models, but growing evidence has highlighted the shortcoming of these model systems in predicting outcomes in more complex downstream animal models, settings required for therapeutic development. Increased understanding of cell to cell interactions and ex vivo growth conditions have allowed researchers to move into more complex ex vivo modeling cultures, such as 3D cell models, with the goal of providing a more natural cellular milieu. In addition, development of 3D cultures with primary cells can also be an avenue to assessing patient specific phenotypes and response to drug treatments.

3D models for studying SARS-CoV-2

Organoid and spheroid models are increasingly being used to more accurately mimic the in vivo cellular microenvironment, bringing more physiological relevance to experimental conditions. Generating organoid and spheroid models can be technically challenging, but once established can offer key insights for translational research projects, as they exhibit gene and protein expression signatures closer to those observed in vivo. 3D organoids are increasingly being used as infection models in lung/airways, gut, kidney, blood vessel, and other tissues to understand mechanisms of infection and immune response, identify key cellular targets, and test potential treatments (2). ​

Create more physiologically relevant 3D cell models in 5 steps ›
Download the free 3D product resource guide ›

References:

  1. Monteil V, Kwon H, Prado P, et al. Inhibition of SARS-CoV-2 Infections in Engineered Human Tissues Using Clinical-Grade Soluble Human ACE2. Cell. 2020;181(4):905‐913.e7.
  2. Ramani A, et al. SARS-CoV-2 targets cortical neurons of 3D human brain organoids and shows neurodegeneration-like effects. bioRxiv 2020.05.20.106575.

Primary cell culture system

Our systems allow you to closely mimic the in vivo state and generate more physiologically relevant data. Each lot of primary cells is performance tested for viability and growth potential.

Accurate cell counts are important for seeding cells for cell-based assays and prior to downstream analysis. The new Countess II FL Automated Cell Counter is a benchtop assay platform equipped with three-channels: brightfield and two optional fluorescence channels for cell counting, monitoring fluorescent protein expression, evaluating apoptosis, and measuring cell viability.

Find cell culture & transfection products for cell line development.

Product Cat No.
Mammalian Cell Culture Reagents Learn more ›

Genetic and phenotypic assessments are required to validate a cellular model in order to ensure its relevance and usability. Various cell types and sources that go through rounds of passaging, extensive engineering, or are exposed to experimental or environmental treatments and conditions need to be characterized. For example, in the case of adult primary stem cells, effects of passaging can influence the gene and protein expression patterns.

Authentication of human cell lines by Short Tandem Repeat analysis

Short tandem repeat (STR) genotyping using capillary electrophoresis is a simple, economical tool in verification of authenticity of human cell lines and primary stem cells and the assessment of the nature of known cell mixtures.  Misidentification of cell lines produces misleading results, confusion, and added costs to research. Journals and funding agencies now require researchers to prove that the cell lines they have used are authentic and have remained so over the course of a study. 

Analysis of highly variable STRs provides a highly specific genetic “fingerprint” of a cell line. Comparing a profile of alleles present at these highly variant loci to known, standardized samples of a cell line provides confidence that the cell line is authentic.  The Applied Biosystems CLA Identifiler Plus and Direct kits have been optimized to analyze 16 highly variant human STRs with amplification time of under three hours.  Applied Biosystems GeneMapper Software 6 and the cloud-based microsatellite analysis (MSA) software solutions facilitate analysis of STRs by making use of pre-established allelic ladders and sizing bin sets for the various STR alleles covered by the Identifiler kits.

Cell health tools for imaging and flow cytometry

Many cell health reagents have applications in both imaging and flow cytometry, such as those that measure toxicity, apoptosis, proliferation, viability, mitochondrial function, and membrane potential, etc.

See cell health reagents for flow cytometry ›
See cell health reagents probes for imaging ›

Genotyping to verify genetic composition

For verification of genetic composition and sequence information of the cell models, PCR enzymes and master mixes serve as fast and efficient tools. Platinum Direct PCR Universal Master Mix offers direct amplification from cell samples without the need to purify DNA, shortening the workflow and reducing hands-on time. Platinum II Taq Hot-Start DNA Polymerase offers fast DNA synthesis and a simplified PCR protocol with a universal annealing temperature, for efficient amplification of target genomic sequences and their analysis by gel electrophoresis or Sanger sequencing.

Power Snap technology

Accelerate viral research with the Power Snap dry precast E-Gel agarose gel technology and run DNA samples in as little as 10 minutes. It is the only benchtop device that seamlessly integrates DNA sample separation and gel visualization into one workflow.

  • Quantitative Proteomics
  • Metabolomics

The worldwide demand for testing of SARS-CoV-2 has created shortage in supplies for qRT-PCR, the current gold standard. Novel approaches that can overcome such shortages and increase testing capacity would be attractive. Mass spectrometry provides number of workflows that can circumvent such issues. Learn more >

  • SRM
  • PRM
  • SureQuant

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Therapeutic discovery & development

Therapeutic discovery and development is a complex process that can begin with screens, targets, or bioactive molecules that jumpstart the development workflow. From ready-to-use antiviral compounds to assays and complex libraries, we are here to support your research and development of potential therapeutics. In addition, our drug discovery and development team provides support, expertise, collaboration, and customization to meet your unique needs.

With over 40 antiviral compounds with proven activity, you can start your search for new antiviral compounds a few steps ahead of the curve, potentially speeding your time to results.

Product  Cat No.  

High-quality compounds with known anti-viral properties from our Alfa Aesar
and Acros Organics brands.
The offering includes over 41 compounds, including: Raltegravir potassium salt
1-Adamantanamine, 98%
Brefeldin A, 99%
Betulinic acid
Oseltamivir phosphate, 98%
Ribavirin, 98%
(+)-5-Iodo-2'-deoxyuridine, 99%
1-Adamantanamine, 96%
Cytosine beta-D-arabinofuranoside, 98%
3'-Azido-3'-deoxythymidine, 98%
Atazanavir
Ganciclovir, 98%
Emtricitabine
9-beta-D-Arabinofuranosyladenine-5'-monophosphate, 99%
Imiquimod, 99%, and many more, in stock at high purity.

Learn more ›

While the number of available full genomes produced by NGS can grow rapidly, datasets have historically faced challenges in the quality of the sequences. High-quality sequences provide coverage of entire genomes to help develop potential anti-viral therapies. In comparison to transposomic methods, the Invitrogen Collibri DNA Library Prep Kits for Illumina Systems consistently provide full coverage of RNA viruses, after reverse transcription, as well as host genomes. The Invitrogen Collibri Stranded RNA Kits for Illumina Systems with Human/Mouse/Rat Depletion attach helper adaptors directly to RNA, achieving robust coverage of the entire transcriptome.

Fragment analysis by capillary electrophoresis enables rapid screening for the presence or absence of SARS-CoV-2 RNA through a simple workflow.  Briefly, purified nucleic acid is mixed with a cocktail of fluorescent primers that are specific to the nucleoprotein (N protein), spike protein (S protein), and orf-1ab sequences in the SARS-CoV-2 genome. Primer pairs in the cocktail have been designed to generate well-separated, gene-specific amplicons. The sample–primer mixture is reverse transcribed and subjected to endpoint PCR in a single reaction. The resulting fragments are separated by size and detected using capillary electrophoresis.

 Protocol: Detection of RNA from SARS-CoV-2 using fragment analysis

The search for bioactive molecules in early-stage drug discovery using rapid compound screening and fragment-based design should not be like looking for a needle in a haystack. The Maybridge collections of screening compounds and fragment libraries offer a high degree of diversity in convenient and customizable formats with chemical properties designed to help accelerate your hit discovery.

Product Cat No.
Antiviral library - over 8,000 compounds  chosen to facilitate the discovery of novel chemical entitites with profound viral activity and imporved safety profiles Learn more ›
Maybridge HitDiscover - a pre-plated collection of over 53,000 screening compounds  that provide the diversity of the entire Maybridge collection. Learn more ›
Maybridge HitFinder - unique, pre-plated selections from the Maybridge collection chosen using  a clustering algorithm, all compounds fit Lipinski guidelines for "drug-likeness". Learn more ›
Maybridge HitCreator - 14,000 compounds pre-plated in 96 or 384-well plates that represent the diversity of a 500,000 compound library distilled to 14,000 molecules.  Learn more ›
Maybridge Fragment Collection includes the overall fragment library as well as a fluor-,  19F-,  bromo-, and a pre-fragment library. Available as the entire library of 2,500 compounds or a core set of 1,000 and a supplemental set of 1,500, as well as cusotmized sets  for your convenience. Learn more ›
Protein-protein interaction library - over 11,000 compounds selected through analysis of the PPI-relebvant chemical space Learn more ›
GPCR library - over 10,000 compounds selected for screenign against G-protein coupled receptors Learn more ›
Kinase library - over 6,000 compounds chosen to facilitate the dsicovery of novel kinase inhibitors from our advanced collection of small molecules, fragments, and macrocycles Learn more ›

With a variety of surfaces optimized to capture the biomolecule of your choice, a wide selection of microplates are available for your immunoassay development needs.

A number of preclinical and clinical studies have been conducted investigating the cellular damage caused by SARS-CoV-2. For example, the immunomodulatory and reparative properties of mesenchymal stem cells could reduce mortality rate by reversing acute inflammation of lungs, inhibiting over-activation of immune cells, protecting lung alveoli epithelial cells, promoting tissue repair, preventing pulmonary fibrosis, or improving lung function. Thermo Fisher Scientific provides key resources to address challenges in the workflow for mesenchymal stem cell clinical research.

MSC media and reagents for cell therapy
Learn more about cell therapy approaches ›
Custom Media
Clinical Trial & Logistics support
GMP Viral Vector Development & Manufacturing Services

Human cells used in cell and gene therapy can be validated by Short tandem repeat (STR) genotyping using capillary electrophoresis. The Applied Biosystems CLA Identifiler Plus and Direct kits have been optimized to analyze 16 highly variant human STRs with amplification time of under three hours. Applied Biosystems GeneMapper Software 6 and the cloud-based microsatellite analysis (MSA) software solutions facilitate analysis of STRs by making use of pre-established allelic ladders and sizing bin sets for the various STR alleles covered by the Identifiler kits.
Learn more about how to use STR analysis to authenticate human cell lines ›

Catalog # Name url
4331182 Hs01085333_m1 / SARS-CoV-2 ACE2
4331182 Hs01122322_m1 / SARS-CoV-2 TMPRSS2
4331182 Hs00947439_m1 / SARS-CoV-2 CTSB
4331182 Hs00964650_m1 / SARS-CoV-2 CTSL
4331182 Hs00174265_m1 / HCoV-229E ANPEP
4331182 Hs00897386_m1 / MERS-CoV DPP4
4331182 Hs00949382_m1 / Influenza ST6GAL1
4331182 Hs00920870_m1 / Influenza ST3GAL4

Bulk and specialty chemical services are available for custom synthesis, packaging, and testing, or for larger scale batches of candidate molecules. 

Learn more ›

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