COVID-19 and Infectious Disease Resources

Critical Tools for Coronavirus (COVID-19) Research

The ongoing coronavirus (COVID-19) outbreak has taken thousands of lives and the number of infections is growing daily. Accelerating our understanding of the adaptive and innate immune response to infectious disease is critical. The translation of this research to drive discovery of broadly neutralizing antibodies and prepare effective vaccination strategies is equally urgent.


Name of Document A


Name of Document B


Name of Document C


Name of Document D


Placing Single Cell and Spatial Biology at the Forefront of Infectious Disease Research

Quickly solving today’s infectious disease challenges requires the application of innovative tools. With single cell and spatial technology, researchers can capture multiple dimensions of infection and the immune response, including cellular phenotypes, adaptive immune repertoire and antigen specificity, spatial resolution of immune tissue infiltration, epigenetic regulation of immune cell activity, and viral interference with the host immune response.

Chromium Single Cell Solutions from 10x Genomics can be applied to the study of hundreds to more than one million single T and B cells on a cell-by-cell basis. The Visium Spatial Gene Expression Solution provides a high-resolution view of gene expression within intact tissue sections to reveal the fundamental molecular and cellular basis for complex pathophysiological signatures. In the sections below, explore a curated list of publications and other helpful resources using these technologies.
Hear from leading Immunologists—Watch our Global Immunology Virtual Summit.

Click here to view our on-demand webinar and learn about important tools for COVID-19 research.

COVID-19 Publications, Pre-Prints & Resources Demonstrating the Application of 10x Solutions

Explore a selection of publications and preprints that showcase the latest research on COVID-19.

Cao et al., 2020, Cell
Reported the rapid identification of SARS-CoV-2 neutralizing antibodies using the Single Cell Immune Profiling Solution from antigen-enriched B cells from 60 convalescent patients. This demonstrates that human neutralizing antibodies could be efficiently discovered by high-throughput single B-cell sequencing in response to pandemic infectious diseases.

Liao et al., 2020 Nature Medicine
Identified highly inflammatory monocyte-derived FCN1+ macrophage activity in bronchoalveolar lavage fluid from COVID-19 patients with severely damaged lungs and expanded clonal CD8+ T cells in patients with mild symptoms using the Single Cell Immune Profiling Solution.

Lukassen et al., 2020, EMBO J
Observed predominant expression of ACE2 in a transient secretory cell type of the subsegmental bronchial branches using the Single Cell Gene Expression Solution using single nuclei and single cells, concluding this cell type may be more vulnerable to SARS-CoV-2 infection.

Zost et al., 2020, Biorxiv
This study describes the methodology used to efficiently generate a large library of highly-functional monoclonal antibodies directed against the SARS-CoV-2 spike (S) protein using the Single Cell Immune Profiling Solution. They identified that most neutralizing mAbs recognize the receptor-binding domain (RBD) of S. This work defines sites of vulnerability on SARS-CoV-2 S and demonstrates the speed and robustness of new antibody discovery methodologies.

Introduced Viral-Track, a computational method that globally scans unmapped scRNA-seq data for the presence of viral RNA, enabling transcriptional cell sorting of infected versus bystander cells using the Single Cell Immune Profiling and Gene Expression Solutions, as well as other methods. The authors applied Viral-Track to Bronchoalveloar-Lavage samples from severe and mild COVID-19 patients and revealed a dramatic impact of the virus on the immune system of severe patients compared to mild cases.

Sungnak et al., 2020 Nature
Investigated SARS-CoV-2 potential tropism by surveying expression of viral entry-associated genes in single-cell RNA-sequencing data, using the Single Cell Gene Expression and Immune Profiling solutions as well as other methods, from multiple tissues from healthy human donors from datasets generated within the Human Cell Atlas (HCA) consortium and other resources. Findings may have important implications for understanding viral transmissibility.

Chua et al., 2020 Medrxiv
Revealed the different types and states of airway epithelial cells that are vulnerable for SARS-CoV-2 infection by performing single cell gene expression analysis of nasopharyngeal and bronchial samples of COVID-19 patients using the Single Cell Gene Expression Solution. The study provides novel insights into the pathophysiology of COVID-19 and suggests an immunomodulatory therapy along the CCL2, CCL3/CCR1 axis to be a promising option to prevent and treat critical course of COVID-19.

Monteil et al., 2020 Cell
Using the Single Cell Gene Expression Solution, demonstrated that clinical grade hrsACE2 reduced SARS-CoV-2 recovery from Vero cells by a factor of 1,000-5,000 and that SARS-CoV-2 can directly infect engineered human blood vessel organoids and human kidney organoids, which can be inhibited by hrsACE2. These data demonstrate that hrsACE2 can significantly block early stages of SARS-CoV-2 infections.

Wen et al., 2020 Nature Cell Discovery
Demonstrated, using the Single Cell Immune Profiling Solution, that COVID-19 induced a unique signature of immune cells, especially in the early recovery stage (ERS) and provides the first evidence of an inflammatory immune signature in the ERS, suggesting COVID-19 patients are still vulnerable after hospital discharge. Identification of novel BCR signaling may lead to the development of vaccines and antibodies for the treatment of COVID-19.

Zang et al, 2020 Science Immunology
Using the Single Cell Gene Expression Solution, demonstrated productive infection of SARS-CoV-2 in ACE2+ mature enterocytes in human small intestinal enteroids and highlights the intestine as a potential site of SARS-CoV-2 replication, which may contribute to local and systemic illness and overall disease progression.

Read more publications highlighting research on COVID-19 →

And explore other infectious disease publications here →


Webinars, Application Notes, and Research Snapshots

Webinars & Presentations
Understand Infectious-Disease-Single-Cell-Immune-Profiling.png
Understand Infectious Disease with Single Cell Immune Profiling
Speaker: Leo Chan, PhD, Staff Field Applications Scientist, 10x Genomics

Learn how single cell immune profiling solutions can be used to understand the biology of infection. Explore research use cases and novel experimental workflows to accelerate antibody discovery and validation in this webinar. Watch now.
An Integral Tool to Accelerate Antibody Discovery
Speaker: Ian Setliff, PhD, Vanderbilt University

Introducing a powerful method of antibody discovery that maps full-length, paired B-cell receptor sequences to antigen specificity in single cells. This is LIBRA-seq. Watch webinar.
Multiomic Profiling of the Response to Influenza Vaccination
Speaker: Sarah Taylor, Staff Scientist, Product Development Lead, 10x Genomics

We profiled 1.3 million cells, including PBMCs, T cells, and B cells, from four human blood samples taken before and after influenza vaccination. Learn how to apply ultra high-throughput single cell capabilities to characterize the immune response to vaccination in this presentation from AGBT 2020. Watch now.

Research Snapshots
10x Genomics customers continue to advance infectious disease research. Explore their findings with our Customer Research Snapshots, documents that highlight customer studies and condense them into easy-to-understand experimental summaries.

10x_LIT071_High-Throughput-Mapping-of-B-Cell-Receptor-Sequences-to-Antigen-Specificity_Letter_Digital (1)-1.jpg
Authors: Setliff et al., 2019

Profiled blood samples from two subjects with HIV, identifying the antigen specificity of thousands of single B cells using LIBRA-seq, a method to rapidly map paired full-length heavy- and light-chain B-cell receptor sequences to their corresponding antigens.

Application Notes
Learn how to characterize multiple dimensions of immune cell biology with these application notes, highlighting validation experiments conducted by 10x Genomics scientists.
A New Way of Exploring Immunity

Gain a more complete understanding of the T-cell receptor-pMHC interaction with single cell immune profiling. Download this application note.

Use multiomic cytometry to measure multiple dimensions of the antigen-specific T-cell response with single cell immune profiling. Download our application note.

Infectious Disease Research at Single Cell and Spatial Resolution with 10x Genomics Solutions

Leveraging DNA barcoding and next-generation sequencing to simultaneously label and analyze diverse biomolecular analytes, single cell and spatial technologies enable researchers to:

Compatible Product Partners

10x Genomics solutions for immunology and infectious disease research are supported by first-in-class compatible product partners. Leverage our Single Cell Immune Profiling Solution with Feature Barcode technology, and the following compatible products, to simultaneously map the immune repertoire, detect cell surface markers, and determine antigen specificity in hundreds to thousands of single T and B cells.

Characterize cell surface proteins with oligo-conjugated antibodies from BioLegend. Explore BioLegend TotalSeq Antibodies for Immunology: All TotalSeq Products and TNBK Panel Products
Detect T-cell receptor antigen specificity with oligo-labeled MHC multimer reagents from Immudex. Leverage Immudex dCODE Dextramer products for your infectious disease research: Assess Coronavirus Immunity.
Logo_MiltenyiBiotec_RGB.jpg We partner with Miltenyi Biotec for sample preparation. Explore their products for cell collection, depletion, and tissue dissociation, and these additional resources for researchers working on the coronavirus.

For more detailed information about how to use 10x Genomics solutions, visit our support page.