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Accurate Single Cell RNA Expression Profiling to Illuminate SARS-CoV-2 Entry and Transmission.

Single-cell sequencing and analyses have been applied in the field of virology, providing new approaches to explore viral diversity and cell response to viral infection, including the widely-spreading SARS-CoV-2 (COVID-19). Empowered by unrivaled expertise and advances in single-cell approaches, SingleX has developed integrated single cell omics solutions to study differences between host cell types and subpopulations which are associated with virus entry and transmission, at single-cell level of genome, transcriptome, epigenome, and proteome.

Why Apply Single-cell Sequencing to SARS-CoV-2 Research?

Single-cell sequencing technologies, i.e., single cell transcriptome sequencing and analyses (scRNA-Seq) have the ability to bring valuable insights into studying viral infection in relation to host cellular heterogeneity.

  • Cellular heterogeneity has been shown to affect virus replication from the initial viral entry to viral release, and also affects the clinical outcome of the viral infection. scRNA-Seq reveals cell heterogeneity which is often masked at a population level.
  • scRNA-Seq can identify transcriptomic signatures hallmarking distinct cell subsets that are relevant for virus-host interactions.
  • scRNA-Seq analyzes the changes of virus transcriptome in different infection states to explore the differences in gene expression and cell environment required for virus latent infection.
  • scRNA-Seq analyzes the expression of viral entry-associated genes from multiple tissues from healthy donors to reveal the potential tropism of SARS-CoV-2.

What Have Been Done?

Angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease (TMPRSS2) are critical for the entry and transmission processes of SARS-CoV-2, acting as the entry receptor and main host cell protease, respectively. To explore the susceptible cell types and potential infection routes of SARS-CoV-2, Zhang, et al. analyzed the coexpression pattern of ACE2 and TMPRSS2 in different cell types in both normal human lungs and the gastrointestinal system based on public single-cell transcriptomics databases. Surprisedly, they found that ACE2 and TMPRSS2 were also coexpressed in esophagus upper cells upper epithelial and gland cells and absorptive enterocytes from the ileum and colon except to the lung alveolar type 2 (AT2) cells, indicating that the digestive system along with the respiratory tract is a potential route of COVID-19. With the research advances and data sharing, more accurate transcriptome landscape is uncovering to explore COVID-19 infection mechanisms and promote the development of vaccine and antibody therapeutics.

Single-cell atlas of the digestive tract and lung tissues. Fig.1 Single-cell atlas of the digestive tract and lung tissues. (Zhang, 2020)


SingleX provides a suite of scRNA-Seq sequencing and analyses services to comprehensively characterize the gene expression changes of different tissues/cells, so as to speculate the possible genes involved in the virus entry, infection mechanisms and conclude which cell type may be more vulnerable to SARS-CoV-2 infection. We can help customers to analyze the impact of cell-to-cell variation on the viral life cycle, by sequencing and analyzing viral sequences or cellular host transcriptome for future SARS-CoV-2 therapeutic strategy development. The general workflow for single-cell sequencing is outlined below. We provide both 10X and Smart-seq platforms for flexible project design.

Simplified scRNA-seq workflow. Fig.2 Simplified scRNA-seq workflow.


  • The original sequencing data
  • Detailed data analysis report

SingleX is dedicated to providing the scRNA-Seq sequencing services to explore the relationships between gene expression variation and cellular function, further elucidate the mechanism of virus entry or transmission. If you have any requirements or questions, please feel free to contact us.


  1. Zhang, H.; et al. Digestive system is a potential route of COVID-19: an analysis of single-cell coexpression pattern of key proteins in viral entry process. Gut. 2020.
  2. Wang, Zhengpin, and Xiaojiang Xu. scRNA-seq Profiling of Human Testes Reveals the Presence of the ACE2 Receptor, A Target for SARS-CoV-2 Infection in Spermatogonia, Leydig and Sertoli Cells. Cells 9.4 (2020): 920.
  3. Sungnak, Waradon.; et al. SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nature Medicine (2020): 1-7.
  4. Pan, Xiu-wu.; et al. Identification of a potential mechanism of acute kidney injury during the COVID-19 outbreak: a study based on single-cell transcriptome analysis. Intensive care medicine (2020): 1.


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