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Epstein–Barr Virus: Biology and Early Infection

Epstein–Barr virus (EBV), also known as human herpesvirus 4 (HHV-4), is a member of the Herpesviridae family, subfamily Gammaherpesvirinae, genus Lymphocryptovirus. EBV was first identified in 1964 in Burkitt’s lymphoma, marking the first clear link between an infectious agent and human cancer. Since then, EBV has become a paradigm for virus–host interaction, viral latency, and virus-driven oncogenesis.

A defining feature of EBV—shared with all herpesviruses—is its ability to establish lifelong persistence. EBV tightly controls host cell metabolism and alternates between two phases of its life cycle: a lytic phase, characterized by productive viral replication, and a latent phase, in which the viral genome persists as an episome in long-lived memory B cells with highly restricted gene expression.

Today, EBV is associated with a broad spectrum of diseases, including:

Hodgkin lymphoma
post-transplant lymphoproliferative disorders (PTLD)
non-Hodgkin lymphomas in HIV-positive individuals
T-cell and NK/T-cell lymphomas
nasopharyngeal carcinoma
certain forms of gastric cancer

Beyond malignancies, EBV causes

infectious mononucleosis and
oral hairy leukoplakia

in immunocompromised patients and has been implicated in the pathogenesis of autoimmune diseases such as systemic lupus erythematosus and multiple sclerosis.

Virion Architecture and Genome Organization

Structurally, EBV closely resembles other herpesviruses. The virion has a diameter of approximately 125 nm and consists of three layers:

A lipid envelope derived from host membranes, studded with host cell surface proteins and viral glycoproteins that determine cell tropism and mediate membrane fusion.
A pseudo-icosahedral nucleocapsid, composed of major and minor capsid proteins assembled into 150 hexamers and 11 pentamers, together with a unique portal protein.
A pleomorphic tegument, consisting of 20–40 viral proteins, positioned between envelope and capsid. Embedded within this layer is the capsid-associated tegument complex (CATC).

The EBV genome within the nucleocapsid is a linear double-stranded DNA molecule of approximately 170–180 kb, encoding 85–100 viral proteins and 44 viral microRNAs. At both termini, the genome contains two complementary regions at the ends of 538 bp terminal repeats (TRs), which anneal and ligate after infection, allowing circularization of the genome into an episome. In addition, four internal repeat regions (IR1–IR4) divide the genome into five unique regions (U1–U5) and are closely linked to EBV’s transforming ability.

Schematic diagram of Epstein-Barr virus labeled with lipid bilayer, nucleocapsid, DNA genome, inner and outer tegument, and various surface proteins.

Cell Tropism and Entry Pathways

EBV exhibits a pronounced tropism for pharyngeal epithelial cells and B lymphocytes, using distinct but related entry mechanisms in each cell type—an important consideration for peptide-based studies of viral entry and antigen presentation.

Entry into Epithelial Cells

In epithelial cells, EBV attachment is initiated by the interaction of the viral glycoprotein BMRF2 with cellular integrins via a conserved RGD (arginine–glycine–aspartate) motif.
A similar integrin-binding motif in gH, as part of the gH/gL complex, further stabilizes virus–cell contact.
Ultimately, gB is recruited and membrane fusion is executed by the conserved herpesviral fusion machinery formed by gH/gL and gB, allowing delivery of the nucleocapsid into the cytoplasm.

Entry into B Lymphocytes

In B cells, initial attachment is mediated by gp350/220*, the most abundant viral glycoprotein, which binds complement receptors CR1 (CD35) or CR2 (CD21) on the B-cell surface. This interaction triggers endocytosis of the virion.

Within the endosome, the viral glycoprotein gp42—part of the heterotrimeric gH/gL/gp42 complex—binds to the β-chain of HLA class II molecules, which are abundantly expressed on B cells. This interaction induces a cascade of conformational changes that enable gL to engage gB, activating gB’s fusogenic activity and leading to fusion of the viral and endosomal membranes.

*gp350/220 are two isoforms of 350 kDa and 220 kDa with identical function. The shorter splice variant gp220 is also named gp340 reflecting historical conventions, assay-dependent detection, and differences in glycosylation.

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Earliest Cytoplasmic and Nuclear Events (Pre-Latent Phase)

Following membrane fusion, the uncoated EBV is released into the cytosol, marking the beginning of the pre-latent phase. At this stage, the outer tegument proteins rapidly dissociate. These proteins are primary effectors: they restrict host protein synthesis, counteract apoptosis, and remodel cellular metabolism to favor viral persistence. Many of them are constitutively produced during the lytic stage, implicating an importance for viral replication.

In contrast, inner tegument proteins, most notably BPLF1, remain in part capsid-associated and interact with the cellular cytoskeleton. Through interactions with dyneins and microtubule plus-end associated proteins (+TIPs), the nucleocapsid is actively transported toward the centrosome near the nucleus. Subsequent trafficking to the nuclear membrane is thought to resemble the mechanism described for herpes simplex virus type 1 (HSV-1), involving nuclear localization signals and interactions with the nuclear pore complex (NPC) – probably mediated by BPLF1.

The delivery of the viral DNA into the nucleus occurs through the nuclear pore and is driven by intracapsid pressure, analogous to genome release in bacteriophages. Once inside the nucleus, the linear EBV genome circularizes via its terminal repeats, forming a stable episome—the molecular foundation for EBV latency and long-term persistence.

Diagram showing a B cell nucleus with cytoskeleton, nuclear membrane, and two viral capsids labeled BPLF-1 and dynein

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Literature

Zaremba, Andrii et al. “A thorough insight into the life cycle of the Epstein-Barr virus. From the molecular to the organismal level.” Current research in microbial sciences vol. 9 100505. 3 Nov. 2025, doi:10.1016/j.crmicr.2025.100505

Feature	MHC Class I	MHC Class II
Peptide source	Endogenous (self, viral, tumor)	Exogenous (bacterial, fungal, parasitic, soluble proteins)
Peptide length	8–10 amino acids	13–25 amino acids
Groove structure	Closed at both ends	Open at both ends
Anchor positions	P2, P9	P1, P4, P6, P9 (+ minor anchors)
Recognized by	CD8⁺ cytotoxic T cells	CD4⁺ helper T cells

Understanding these differences is critical for designing peptide-based vaccines, T cell assays, and epitope mapping strategies that align with either class I or class II presentation pathways.

MHC Class I

acts as a transporter between the cytoplasmic compartment and the cell surface. It primarily presents endogenous antigens — proteins that are newly synthesized within the cell, including self-antigens, viral peptides, and tumor-associated antigens.

These proteins are partially degraded in the cytoplasm by the proteasome, transported into the endoplasmic reticulum via TAP (Transporter associated with Antigen Processing), and loaded onto MHC class I molecules before being displayed on the cell surface.

Thus, CD8⁺ T cells mainly recognize endogenously derived peptides, allowing them to monitor the intracellular health of the organism and eliminate infected or transformed cells.

Drawing of a cell with endogenous tumor or viral antigens, its MHC class I molecule and a recognising T cell receptor

MHC Class II

by contrast, functions as a transport system between endosomes and the cell surface. It presents exogenous antigens — proteins that originate from outside the cell.

These foreign particles, such as bacterial, fungal, or parasitic proteins, as well as soluble antigens, are internalized via endocytosis and degraded into peptides within the endosomal compartment.

The MHC class II molecule then binds these peptides and transports them to the cell surface, where they are presented to CD4⁺ T helper cells, which orchestrate immune responses through cytokine release and B cell activation.

Drawing of a cell taking up exogenous bacterial, fungal or parasitic antigens, its MHC class II molecule and a recognising T cell receptor

MHC Class I: A Closed Groove with Defined Peptide Length

The MHC class I binding groove is closed at both ends, which restricts the length of peptides it can accommodate. Typically, MHCI binds short peptides of 8–10 amino acids, most often nonamers.

Peptides bind in an extended conformation, depending on anchor residues—specific amino acids that fit into deep hydrophobic pockets, most commonly at positions P2 and P9.

These anchor interactions stabilize the peptide–MHC complex, while exposed residues project upward to interact with the T cell receptor (TCR) and determine antigen specificity.

Drawing of the MHC class I binding groove binding a nonamer peptide

MHC Class II: An Open Groove with Extended Peptide Binding

In contrast, the MHC class II binding groove is open at both ends, allowing peptides of variable lengths (typically 13–25 amino acids) to bind. The peptides can extend beyond the groove, resulting in more flexible and diverse antigen presentation to CD4⁺ T cells.

The bound peptide typically adopts a type II polyproline helix [3, 4 in Ferrante, 2007] conformation that fits into specific binding pockets within the MHC class II molecule. Major anchor positions are located at P1, P4, P6, and P9, where the side chains of certain amino acids interact with deep, hydrophobic or charged pockets in the MHC molecule:

P1: often accommodates an aromatic amino acid (e.g., phenylalanine, tyrosine, or tryptophan)
P4: typically binds a hydrophobic or polar/charged amino acid
P6: recognizes an amino acid specific to the individual MHC II allele
P9: prefers a hydrophobic amino acid

Minor anchor residues at positions such as P2, P3, P7, and P10 can further stabilize the interaction.

Drawing of the MHC class II binding groove binding a 13-mer peptide

Drawing of the MHC class II binding groove binding a 13-mer peptide