Why Epstein Barr Virus Lingers Dangerously in Some People

Imagine a virus that infects nearly everyone on the planet by adulthood, yet behaves like a harmless hitchhiker in most cases only to wreak havoc in a select few, contributing to everything from autoimmune diseases to cancers. That is the story of the Epstein–Barr virus (EBV), the notorious culprit behind infectious mononucleosis, or “mono,” the exhausting illness that often plagues teenagers with fever, sore throat, and swollen glands.

For about 90% of adults worldwide, EBV settles into a lifelong dormant state after the initial infection, kept in check by the immune system. But for an unlucky minority, the virus persists at higher levels, potentially fueling chronic conditions such as multiple sclerosis (MS), lupus, and certain lymphomas.

Why does this common herpesvirus part of the same viral family as the chickenpox virus remain silent in some people but turn dangerous in others?

Study published in Nature in January 2026 offers new answers, revealing how genetic differences shape the body’s ability to control EBV and why viral persistence may raise the risk of long-term disease.

Table of Contents

Digging for Viral Gold in Genomic “Junk”

Instead of collecting new samples, researchers first reanalyzed existing whole genome sequencing (WGS) data from two massive population biobanks. Specifically, the study examined DNA from over 490,000 participants in the UK Biobank and in addition more than 245,000 individuals from a U.S. national research cohort. As a result, this approach produced the largest EBV genomic study conducted to date.

During standard genome sequencing, fragments that do not match human DNA are typically discarded. The researchers took a different approach. They searched this overlooked data for EBV genetic material, aligning discarded reads to the EBV genome and estimating viral DNA levels in blood samples.

They identified persistent low-level viral circulation termed EBV DNAemia in roughly 10–12% of participants. This did not indicate active infection but rather periodic reactivation of latent virus. Validation analyses confirmed strong associations between detectable EBV DNA and prior EBV exposure.

According to the researchers, genetic variation plays a key role in determining how effectively the immune system keeps the virus under control, and poorer control appears to be linked with multiple chronic illnesses.

22 Independent Loci Shape Viral Persistence

Using genome-wide association studies (GWAS), the team identified 22 independent genetic regions significantly associated with EBV persistence. Most of the strongest signals were located in the Human Leukocyte Antigen (HLA) region on chromosome 6.

HLA genes encode major histocompatibility complex (MHC) proteins, which present viral fragments to immune cells. Certain HLA variants appear to reduce the immune system’s ability to recognize EBV-infected cells, allowing the virus to persist. In contrast, protective variants bind EBV antigens more effectively, improving immune clearance.

An expanded genetic analysis also identified protein-altering variants in 148 immune-related genes, many involved in antigen processing, T-cell regulation, and antiviral defense. Although genetics accounted for a modest proportion of overall risk, the strongest effects were concentrated in immune pathways.

Key Genes Implicated in EBV Control

Gene	Primary Role	Relevance to EBV
SLAMF7	Activates natural killer (NK) cells	Reduced killing of EBV-infected cells
CTLA4	Regulates T-cell immune balance	May allow viral persistence
EOMES	Controls T-cell differentiation	Linked to chronic infection susceptibility
PTPN22	Immune signaling regulator	Associated with autoimmune risk
BCL2L11 (BIM)	Promotes immune cell apoptosis	Affects clearance of infected cells
GSDMB	Inflammatory cell death	Potential antiviral role
TERT	Telomere maintenance	May influence EBV-driven B-cell survival
LNPEP	Antigen processing	Impairs EBV peptide presentation

Single-cell analyses revealed that these genes are highly active in B cells, dendritic cells, and T cells—the core immune cell types responsible for EBV surveillance.

Connecting Viral Persistence to Disease

To explore clinical relevance, the researchers conducted phenome-wide association analyses linking EBV DNAemia to disease outcomes. Elevated viral levels were associated with over 140 health conditions, including:

Autoimmune diseases: Rheumatoid arthritis, systemic lupus erythematosus, multiple sclerosis
Cancers: Hodgkin lymphoma, splenic malignancies
Respiratory diseases: Chronic obstructive pulmonary disease and emphysema
Neurological conditions: Stroke, dementia, neuromyelitis optica
Mental health: Depressive episodes
Cardiovascular disease: Ischemic heart disease, peripheral vascular disease
Other outcomes: Acute kidney failure, chronic fatigue, tachycardia

Many of these associations were replicated in an independent cohort, strengthening confidence in the findings. However, the authors caution that these results show correlation, not causation. EBV persistence may reflect broader immune dysfunction rather than directly causing disease.

New Era for Viral Research and Personalized Medicine

This study introduces a powerful, cost-effective framework for studying persistent viruses by reanalyzing existing genomic data. The same approach could be applied to other latent viruses implicated in chronic disease and cancer.

Clinically, these findings raise the possibility of genetic screening for EBV control, targeted vaccines, or immune-modulating therapies tailored to individual risk profiles. Drugs that influence immune checkpoints, already used in cancer treatment, may also prove relevant in managing viral persistence.

By revealing how human genetics and ancient viruses interact, this research deepens our understanding of chronic disease and moves medicine closer to truly personalized prevention strategies.