What scRNA-seq Can Tell Us About COVID-19 Immunity

By Jane Cook
October 13, 2021

Asymptomatic COVID Cases: An Immunological Puzzle

A phenomenon puzzling doctors and immunologists since the start of the COVID-19 pandemic is why some people who get exposed to relatively large quantities of virus do not get sick.

These asymptomatic cases provide a unique opportunity to study what makes up the most effective immune response to SARS CoV-2, potentially highlighting new treatment areas or even preventative medicines.

But how can you identify all of the factors contributing to something as complex as the immune response?

A study published in Cell Discovery used scRNA-seq to characterize the local immune response in the nasopharynx, one of the primary sites of COVID-19 infection. The scRNA-seq data was compared between healthy patients, early and late samples of asymptomatic carriers, mild and severely ill COVID patients.

scRNA-seq Reveals a Unique Immune Response

Based on transcriptomic markers, the data could be further categorized into immune response genes and epithelial remodeling signatures, which is where the secrets of the asymptomatic immune response were hidden.

From the scRNA-seq data, there were three clear differences in asymptomatic COVID carriers.

The first barrier to any infection is the epithelium, a layer of protective cells coating the inside of the nose, throat, gut and other vulnerable tissues where viruses can enter cells. In this study, the data showed that epithelial remodeling to strengthen the barrier function of epithelial cells was increased in asymptomatic COVID carriers.

Secondly, inflammation was only marginally increased- enough to recruit more macrophages, a type of immune cell that can “eat” infected cells and viruses, but not so increased that it would start producing the damaging “cytokine storm” seen in severe COVID cases.

Finally, there was a huge increase in CD8+ T-cells in the nasopharyngeal tissue being tested in this study. CD8+ T-cells include cytotoxic T-cells, which are cells that specifically kill virus infected cells to clear an infection.

Ability to fight off COVID

These three factors were the clearest candidates from the scRNA-seq data to be the reasons for the success of the asymptomatic carriers’ immune response and ability to fight off COVID without developing symptoms.

The advanced bioinformatic analysis used in this study illustrates the power of genomic analysis techniques in all aspects of medicine. Constantly improving computational methods and the development of new, custom pipelines will allow researchers to pull more and more information out of scRNA-seq data.

Jane Cook, Journalist & Content Writer, Bridge Informatics

Jane is a Content Writer at Bridge Informatics, a professional services firm that helps biotech customers implement advanced techniques in management and analysis of genomic data. Bridge Informatics focuses on data mining, machine learning, and various bioinformatic techniques to discover biomarkers and companion diagnostics. If you’re interested in reaching out, please email daniel.dacey@old.bridgeinformatics.com or dan.ryder@old.bridgeinformatics.com.



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