CMV infection and its impact on the adaptive immune system

An image of CMV viral particles to depict their impact on the adaptive immune system..
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    Cytomegalovirus (CMV) is a globally widespread virus with a seroprevalence of 50–100%. (1–3) CMV can be transmitted from an infected person via body fluids (e.g. saliva, breast milk, blood, semen, and vaginal secretions). While CMV infection is typically asymptomatic in immunocompetent individuals, it may lead to an increased risk of cancer progression and other diseases, as well as impact on longevity, and can have severe consequences in immunocompromised populations. (1–5)

    CMV is an important cause of morbidity and mortality in people living with HIV/AIDS and in transplant recipients. (4,6) Furthermore, congenital CMV infection, in which CMV is transmitted from a seropositive mother to their fetus, is the leading non-genetic cause of hearing loss in children. (6,7)

    Figure 1 shows the disease mechanisms of CMV and highlights how CMV is particularly relevant in immunosuppressed individuals, including people living with HIV/AVIDS, and during pregnancy.

    Figure 1. CMV disease mechanisms. Adapted from Boeckh et al. (2) GVHD: graft versus host disease.

    CMV infection is not only important for immunocompromised individuals but may also have important implications for the health of immunocompetent individuals. CMV has been linked to cancer development and progression, with the identification of pro-oncogenic CMV proteins and observations of transformation of CMV-infected cells in vitro. (8) It has also been associated with an increased incidence of cardiovascular disease (9) and all-cause mortality in the elderly. (20)

    Understanding T cell responses to CMV infection

    Unlike many other viral infections, which are cleared by the immune system, CMV persists in an individual and can remain latent for a lifetime. This persistence and latency are part of an intricate virus–host interplay as the virus strives to survive while the host tries to suppress viral replication. (2,6,11) In this way, CMV stimulates the immune system to remain on constant alert.

    CMV infection is associated with increases in pro-inflammatory cytokines, as well as significant remodeling of the T-cell repertoire. Typically, after clearance of acute viral infection, the virus-specific T-cell population contracts, with a small portion differentiating into memory T cells.

    However, persistent viral infections like CMV drive the expansion of memory T cells. Virus-specific T cells do not decrease but accumulate at a high frequency in a process known as T-cell memory inflation. (12,13) As a result, CMV-specific T-cell clones can constitute 10–40% of the T-cell repertoire. (7,13) Persistent antigen exposure, as in the case of latent CMV infection, can ultimately lead to T-cell exhaustion and a diminished cytotoxic T-cell response (Figure 2). (13) This can increase susceptibility to other infections and reduce responsiveness to vaccinations. (12)

    An image to depict T cell responses to CMV

    Figure 2. Normally, in acute infection (A), virus-specific CD8+ T cells expand and contract, leaving behind a small population of memory T cells to recognize subsequent viral exposure. In a persistent infection like CMV (B), numbers of virus-specific CD8+ T cells remain high and can constitute a significant portion of the T-cell repertoire. Adapted from Taylor-Robinson and Chapman. (13) APC: antigen-presenting cell; MHC: major histocompatibility complex.

    Given the high global seroprevalence of CMV, as well as the current COVID-19 pandemic, researchers need to understand if and how a subject’s immune system has been affected by CMV. This information can help to contextualize, for example, the results of vaccine or transplant studies because subjects exposed to CMV may have different responses versus those who have not been exposed.

    Uncovering the impact of CMV infection with the immunoSEQ® Assay

    What is the immunoSEQ Assay?

    The immunoSEQ Assay is a highly sensitive, quantitative, and cost-effective multiplex PCR-based method that can sequence the entire T-cell repertoire from a variety of sample types, including but not limited to peripheral blood mononuclear cells (PBMCs), whole blood, and/or formalin-fixed paraffin-embedded (FFPE) tissue.

    Each immunoSEQ Assay contains rigorously designed synthetic immune templates as in-line controls plus optimized primers that ensure accurate, quantitative, and unbiased results with batch-to-batch consistency. It sequences the highly variable genomic complementarity determining region 3 (CDR3) of T-cell receptors (TCRs) and B-cell receptors (BCRs), which can be used as a unique barcode for each cell (Figure 3).

    To learn more about this technology, view our webinar on Exploring Repertoire Development and Dynamics with the immunoSEQ Assay.

    Figure 3. Somatic recombination in the V(D)J region of TCRs and BCRs creates unique DNA barcodes that can be analyzed by the immunoSEQ Assay to profile the adaptive immune system.

    The power of the immunoSEQ Assay has been harnessed to investigate and characterize the effects of CMV infection on the T-cell repertoire. In the next few sections, we will review several studies that have investigated how CMV status affects the T-cell repertoire during aging, as well as how the CMV status of bone marrow and stem cell transplant donors can impact the outcomes of transplant recipients.

    Age-related impacts of CMV infection on the T-cell repertoire

    Most people have likely lived with CMV for decades, and their immune systems have been shaped by CMV. CMV seropositivity and high CMV antibody titers have been independently associated with increased mortality in the elderly. (14) This relationship is thought to be due to the massive CMV-specific CD8+ T-cell response. (6)

    One explanation for the association between CMV infection and mortality is that the expansion of CMV-specific CD8+ T cells decreases repertoire diversity over time. If non-CMV-specific T-cell clones are excluded from the repertoire, this could put people at higher risk of new infections. (6)

    Lindau et al. (12) sequenced the CDR3 of the TCRB chain from PBMCs isolated from 543 individuals of different age groups with known CMV serostatus to investigate the effects of aging on the T-cell repertoire.

    The immunoSEQ Data showed that while CMV does increase the proportion of CD8+ T cells, memory T-cell clones stimulated by persistent CMV infection do not continue to increase in number with age (Figure 4). Overall, the study found that the T-cell repertoire grows to accommodate CMV-driven expansions. Thus, CMV infection did not negatively affect repertoire diversity in the elderly in this study and may not be the mechanism by which CMV is associated with increased mortality in the elderly. (12)

    Figure 4. How CMV impacts the proportion of large clones across different age groups. The boxplots compare the proportion of the most numerous 0.1% of T-cell clones of both CMV+ and CMV subjects. Adapted from Lindau et al. (12)

    Effect of CMV status of donors in bone marrow and stem cell transplants

    Reconstitution of the immune system following hematopoietic stem cell transplant (HSCT) is critical for the recovery and long-term survival of transplant recipients. Monitoring this reconstitution and investigating how donor factors, such as CMV serostatus, can affect reconstitution and recovery can help predict outcomes. CMV reactivation is one of the main causes of morbidity and mortality following HSCT, so understanding how the seropositivity of donors and recipients can impact the T-cell repertoire can help our understanding of what determines outcomes following transplants.

    The ability of the immunoSEQ Assay to track clones longitudinally and compare clones between samples makes it ideal for monitoring immune reconstitution post-transplant. Gaballa et al. (8) were interested in following the reconstitution of γδ T cells, unconventional T cells that express TCRs formed by γ and δ chains. Reconstitution of γδ T cells following allogeneic HSCT has been associated with favorable outcomes (15) and has been shown to play a role in CMV immune surveillance; however, the underlying mechanisms are not fully understood. (16)

    Therefore, to characterize the TCRG CDR3 clonotypes and to reveal any potential CMV-driven differences in TCR diversity, Gaballa et al. (8) analyzed bone marrow graft γδ T cells from seven CMV seropositive donors and nine CMV seronegative donors using the immunoSEQ Assay to sequence the TCRG chain.

    They found that the CMV seropositive bone marrow grafts exhibited reduced TCRG diversity and high clonality. Moreover, CMV seropositive grafts contained a reduced frequency of singleton clones (i.e. clones that appear only once in the sample).

    In addition, the immunoSEQ Data from this study also showed that CMV seropositive graft samples contained a higher proportion of clones with a TCRG gene of 7–12 amino acids in length while CMV seronegative samples were enriched for clones with a TCRG gene of 14 amino acids in length. Taken together, these data illustrate high clonal focusing in CMV seropositive samples, helping to enhance our understanding of how the γδ T-cell repertoire in bone marrow grafts is reshaped by the donor’s CMV serostatus. (8)

    In a separate study, Arruda et al. (17) used the immunoSEQ Assay to sequence the TCRG repertoire of γδ T cells within peripheral blood stem cell grafts in 20 acute myeloid leukemia patients to further understand the impact of CMV on the compartment. They showed that CMV seropositive donors exhibited a reshaped TCRG repertoire with reduced TCRG diversity and increased clonality in CMV seropositive grafts.

    Twelve public sequences were identified in non-relapse patients, which may help us understand factors associated with survival. The incidence of acute graft-versus-host disease was not shown to be correlated with the reshaping of the TCRG repertoire. (17) Together, these studies are helping further our understanding of survival following bone marrow and HSCT and how CMV serostatus may impact the TCR repertoire and overall survival of transplant recipients.

    Identifying T-cell-related signatures of CMV exposure

    Given that CMV alters the T-cell repertoire, knowing the changes that CMV infection elicits means that it is theoretically possible to analyze an individual’s T-cell repertoire and determine whether a person has been exposed to CMV. Emerson et al. (18) used the immunoSEQ Assay to sequence the TCRB chain in 641 healthy individuals with known CMV serostatus in the USA (Figure 5).

    Among the >89 million unique TCRB sequences identified by the immunoSEQ Assay, 488 had been previously identified as CMV reactive. Most of these 488 sequences were similarly expressed among CMV+ and CMV subjects; however, 9 CMV-reactive TCRB sequences were preferentially expressed among CMV+ subjects. (18)

    Figure 5. Experimental overview of how the immunoSEQ Assay was leveraged to develop a T-cell-based signature of CMV serostatus. Adapted from Emerson et al. (18)

    Using these data, the authors were able to develop a classifier capable of inferring a subject’s CMV serostatus. This T-cell signature of CMV exposure was validated in a separate cohort of 120 individuals with unknown CMV serostatus. (18)

    This validated CMV T-cell signature could help advance our understanding of the impacts of CMV seropositivity in health, disease, and mortality by showing how CMV affects the T-cell repertoire and potentially providing a novel way to identify CMV serostatus.

    The immunoSEQ CMV Classifier

    This validated T-cell signature underpins the recently launched immunoSEQ CMV Classifier, which can infer a subject’s CMV serostatus with a simple positive or negative result.

    Using this classifier, researchers can detect past CMV-specific immune responses, study the CMV specific-immune response in many sample types, understand the relationship between CMV and other diseases, and explore the impact of CMV infection on other infectious diseases, autoimmune disease, transplantation, and oncology.

    The applications of the classifier are wide ranging, and include:

    • Capturing the differences or similarities in T-cell immune responses to various diseases in the context of CMV.
    • Understanding the relationship between CMV infection and autoimmune response or the development of autoimmune disease.
    • Assessing the relationship between immunotherapy outcomes and CMV status.

    Discover more about the immunoSEQ CMV Classifier, including how it can enhance your research, here.


    The immune system is continually being altered by the pathogens we encounter. These changes can impact the way the immune system functions, ultimately affecting the way individuals respond to infections, vaccines, and immune-related therapies, as well as natural aging.

    Therefore, for researchers studying the adaptive immune system, it is important to understand how a subject’s immune system may have been shaped by the pathogens they have encountered. The immunoSEQ Assay provides a robust, scalable, flexible, cost-effective, reproducible, and quantitative assessment of the T-cell repertoire. It can analyze both gDNA and cDNA derived from a variety of sample types, including but not limited to PBMCs, whole blood, and FFPE tissue.

    Collecting and analyzing immunoSEQ Data requires no special equipment or expertise in immunology. We can assist through every step of the process, from experimental design to producing publication-ready data.

    We are here to help accelerate your research. For more information, visit our immunoSEQ Assay products page. If you have questions about how to get started, get in touch with our product team.

    For Research Use Only. Not for use in diagnostic procedures.


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