Single-Cell Transcriptomics Unravels the Mystery of HCMV Infection

What is human cytomegalovirus (HCMV)?

You may not have heard of HCMV, but you may have been infected with it. HCMV is an extremely common virus in the herpes family, with estimates that around 60% of adults in developed countries have been infected. Like many other herpesviruses, HCMV infection is mostly asymptomatic, but incurable – once you have a HCMV infection, the virus permanently resides in your cells.

Latent VS Active HCMV

Unfortunately, HCMV does not always stay in its latent form. When triggered into an active infection, most commonly in immunocompromised or pregnant individuals, symptoms can be severe and even fatal. The molecular mechanisms dictating these outcomes, termed productive (active) or non-productive (latent) infections, are poorly understood.

Evidence to-date suggests that a key determinant of the activity of an HCMV infection is the cell type infected by the virus. Monocytes and early myeloid progenitor cells appear to be reservoirs for latent infection, while fully differentiated myeloid cells like macrophages appear to be permissive to active infection, but the mechanism behind this difference remains unknown.

Single-Cell Transcriptomics Identifies Key Viral Genes in HCMV Infection

In a recent paper published in Nature Microbiology, Schwartz et. al. applied single-cell transcriptomics to assess HCMV infection progression in monocytes and macrophages. They found that early expression levels of viral genes IE1 and IE2 were strongly associated with active infection, and the major factor for dictating the type of infection.

The authors also found that intrinsic interferon levels, a main immune cell signaling pathway, were downregulated in macrophages that were permissive to active infection. Their findings suggest dramatically different transcriptional profiles are a main driver of whether or not a cell produces a productive HCMV response, and explains why a weakened immune system could induce an active infection by altering immune cell signaling. Overall these results provide interesting targets to fully characterize the biological mechanisms underlying these gene expression changes.

Outsourcing Bioinformatics Analysis: How Bridge Informatics Can Help

Many of our clients at Bridge Informatics are pursuing these kinds of research questions with sophisticated bioinformatics approaches, and single-cell transcriptomics is one of the most popular analysis types. From pipeline development and software engineering to deploying existing bioinformatics tools, Bridge Informatics can help you on every step of your research journey. 
As experts across data types from cutting-edge sequencing platforms, we can help you tackle the challenging computational tasks of storing, analyzing and interpreting genomic and transcriptomic data. Bridge Informatics’ bioinformaticians are trained bench biologists, so they understand the biological questions driving your computational analysis. Click here to schedule a free introductory call with a member of our team.

Jane Cook, Biochemist & Content Writer, Bridge Informatics

Jane Cook, leading Content Writer for Bridge Informatics, has written over 100 articles on the latest topics and trends for the bioinformatics community. Jane’s broad and deep interdisciplinary molecular biology experience spans developing biochemistry assays to genomics. Prior to joining Bridge, Jane held research assistant roles in biochemistry research labs across a variety of therapeutic areas. While obtaining her B.A. in Biochemistry from Trinity College in Dublin, Ireland, Jane also studied journalism at New York University’s Arthur L. Carter Journalism Institute. As a native Texan, she embraces any challenge that comes her way. Jane hails from Dallas but returns to Ireland any and every chance she gets. If you’re interested in reaching out, please email or

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