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Polyomaviridae
Micrograph showing a polyomavirus infected cell—large (blue) cell below-center-left. Urine cytology specimen.
Virus classification Edit this classification
(unranked): Virus
Realm: Monodnaviria
Kingdom: Shotokuvirae
Phylum: Cossaviricota
Class: Papovaviricetes
Order: Sepolyvirales
Family: Polyomaviridae
Genera

See text

Polyomaviridae is a family of DNA viruses whose natural hosts are mammals and birds.[1][2] As of 2024, there are eight recognized genera.[3] Fourteen species are known to infect humans, while others, such as Simian Virus 40, have been identified in humans to a lesser extent.[4][5] Most of these viruses are very common and typically asymptomatic in most human populations studied.[6][7] BK virus is associated with nephropathy in renal transplant and non-renal solid organ transplant patients,[8][9] JC virus with progressive multifocal leukoencephalopathy,[10] and Merkel cell virus with Merkel cell cancer.[11]

Structure and genome

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A rendering of an icosahedral viral capsid comprising 72 pentamers of murine polyomavirus VP1, colored such that areas of the surface closer to the interior center appear blue and areas nearer to the surface appear red. Rendered from PDB: 1SIE​.

Polyomaviruses are non-enveloped double-stranded DNA viruses with circular genomes of around 5000 base pairs. With such a small size, they are ranked among the smallest known double stranded DNA viruses.[12] The genome is packaged in a viral capsid of about 40-50 nanometers in diameter, which is icosahedral in shape (T=7 symmetry).[2][13] The capsid is composed of 72 pentameric capsomeres of a protein called VP1, which is capable of self-assembly into a closed icosahedron;[14] each pentamer of VP1 is associated with one molecule of one of the other two capsid proteins, VP2 or VP3.[5]

Genome structure of the WU virus, a human polyomavirus. The early region is shown on the left and contains the TAg (tumor antigen) proteins; the late region is on the right and contains the capsid proteins.[15]

The genome of a typical polyomavirus codes for between five and nine proteins, divided into two transcriptional regions called the early and late regions due to the time during infection in which they are transcribed. Each region is transcribed by the host cell's RNA polymerase II as a single pre-messenger RNA containing multiple genes. The early region usually codes for two proteins, the small and large tumor antigens, produced by alternative splicing. The late region contains the three capsid structural proteins VP1, VP2, and VP3, produced by alternative translational start sites. Additional genes and other variations on this theme are present in some viruses: for example, rodent polyomaviruses have a third protein called middle tumor antigen in the early region, which is extremely efficient at inducing cellular transformation; SV40 has an additional capsid protein VP4; some examples have an additional regulatory protein called agnoprotein expressed from the late region. The genome also contains a non-coding control or regulatory region containing the early and late regions' promoters, transcriptional start sites, and the origin of replication.[2][13][5][16]

Replication and life cycle

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Murine polyomavirus VP1 in complex with the GT1a glycan. GT1a is shown in yellow and the VP1 monomer with a white surface and a blue protein backbone. A complex network of hydrogen bonds, many water-mediated, is shown at the binding surface by orange lines, with participating protein residues shown as sticks. Mutations of the two residues shown in cyan at the bottom of the figure can significantly affect pathogenicity. From PDB: 5CPW​.[17]

The polyomavirus life cycle begins with entry into a host cell. Cellular receptors for polyomaviruses are sialic acid residues of glycans, commonly gangliosides. The attachment of polyomaviruses to host cells is mediated by the binding of VP1 to sialylated glycans on the cell surface.[2][13][16][17] In some particular viruses, additional cell-surface interactions occur; for example, the JC virus is believed to require interaction with the 5HT2A receptor and the Merkel cell virus with heparan sulfate.[16][18] However, in general virus-cell interactions are mediated by commonly occurring molecules on the cell surface, and therefore are likely not a major contributor to individual viruses' observed cell-type tropism.[16] After binding to molecules on the cell surface, the virion is endocytosed and enters the endoplasmic reticulum - a behavior unique among known non-enveloped viruses[19] - where the viral capsid structure is likely to be disrupted by action of host cell disulfide isomerase enzymes.[2][13][20]

The details of transit to the nucleus are not clear and may vary among individual polyomaviruses. It has been frequently reported that an intact, albeit distorted, virion particle is released from the endoplasmic reticulum into the cell cytoplasm, where the genome is released from the capsid, possibly due to the low calcium concentration in the cytoplasm.[19] Both expression of viral genes and replication of the viral genome occur in the nucleus using host cell machinery. The early genes - comprising at minimum the small tumor antigen (ST) and large tumor antigen (LT) - are expressed first, from a single alternatively spliced messenger RNA strand. These proteins serve to manipulate the host's cell cycle - dysregulating the transition from G1 phase to S phase, when the host cell's genome is replicated - because host cell DNA replication machinery is needed for viral genome replication.[2][13][16] The precise mechanism of this dysregulation depends on the virus; for example, SV40 LT can directly bind host cell p53, but murine polyomavirus LT does not.[21] LT induces DNA replication from the viral genome's non-coding control region (NCCR), after which expression of the early mRNA is reduced and expression of the late mRNA, which encodes the viral capsid proteins, begins.[20] As these interactions begin, the LTs belonging to several polyomaviruses, including Merkel cell polyomavirus, present oncogenic potential.[22] Several mechanisms have been described for regulating the transition from early to late gene expression, including the involvement of the LT protein in repressing the early promoter,[20] the expression of un-terminated late mRNAs with extensions complementary to early mRNA,[16] and the expression of regulatory microRNA.[16] Expression of the late genes results in accumulation of the viral capsid proteins in the host cell cytoplasm. Capsid components enter the nucleus in order to encapsidate new viral genomic DNA. New virions may be assembled in viral factories.[2][13] The mechanism of viral release from the host cell varies among polyomaviruses; some express proteins that facilitate cell exit, such as the agnoprotein or VP4.[20] In some cases high levels of encapsidated virus result in cell lysis, releasing the virions.[16]

Viral proteins

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Tumor antigens

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The large tumor antigen plays a key role in regulating the viral life cycle by binding to the viral origin of DNA replication where it promotes DNA synthesis. Also as the polyomavirus relies on the host cell machinery to replicate the host cell needs to be in s-phase for this to begin. Due to this, large T-antigen also modulates cellular signaling pathways to stimulate progression of the cell cycle by binding to a number of cellular control proteins.[23] This is achieved by a two prong attack of inhibiting tumor suppressing genes p53 and members of the retinoblastoma (pRB) family,[24] and stimulating cell growth pathways by binding cellular DNA, ATPase-helicase, DNA polymerase α association, and binding of transcription preinitiation complex factors.[25] This abnormal stimulation of the cell cycle is a powerful force for oncogenic transformation.[citation needed]

The small tumor antigen protein is also able to activate several cellular pathways that stimulate cell proliferation. Polyomavirus small T antigens commonly target protein phosphatase 2A (PP2A),[26] a key multisubunit regulator of multiple pathways including Akt, the mitogen-activated protein kinase (MAPK) pathway, and the stress-activated protein kinase (SAPK) pathway.[27][28] Merkel cell polyomavirus small T antigen encodes a unique domain, called the LT-stabilization domain (LSD), that binds to and inhibits the FBXW7 E3 ligase regulating both cellular and viral oncoproteins.[29] Unlike for SV40, the MCV small T antigen directly transforms rodent cells in vitro.[30]

The middle tumor antigen is used in model organisms developed to study cancer, such as the MMTV-PyMT system where middle T is coupled to the MMTV promoter. There it functions as an oncogene, while the tissue where the tumor develops is determined by the MMTV promoter.[citation needed]

Capsid proteins

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The polyomavirus capsid consists of one major component, major capsid protein VP1, and one or two minor components, minor capsid proteins VP2 and VP3. VP1 pentamers form the closed icosahedral viral capsid, and in the interior of the capsid each pentamer is associated with one molecule of either VP2 or VP3.[5][31] Some polyomaviruses, such as Merkel cell polyomavirus, do not encode or express VP3.[32] The capsid proteins are expressed from the late region of the genome.[5]

Agnoprotein

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The agnoprotein is a small multifunctional phospho-protein found in the late coding part of the genome of some polyomaviruses, most notably BK virus, JC virus, and SV40. It is essential for proliferation in the viruses that express it and is thought to be involved in regulating the viral life cycle, particularly replication and viral exit from the host cell, but the exact mechanisms are unclear.[33][34]

Taxonomy

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The polyomaviruses are members of group I (dsDNA viruses). The classification of polyomaviruses has been the subject of several proposed revisions as new members of the group are discovered. Formerly, polyomaviruses and papillomaviruses, which share many structural features but have very different genomic organizations, were classified together in the now-obsolete family Papovaviridae.[35] (The name Papovaviridae derived from three abbreviations: Pa for Papillomavirus, Po for Polyomavirus, and Va for "vacuolating.")[36] The polyomaviruses were divided into three major clades (that is, genetically related groups): the SV40 clade, the avian clade, and the murine polyomavirus clade.[37]

The family contains the following genera:[38]

Description of additional viruses is ongoing. These include the sea otter polyomavirus 1[39] and Alpaca polyomavirus[40] Another virus is the giant panda polyomavirus 1.[41] Another virus has been described from sigmodontine rodents.[42] Another - tree shrew polyomavirus 1 - has been described in the tree shrew.[43]

Human polyomaviruses

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Most polyomaviruses do not infect humans. Of the polyomaviruses cataloged as of 2017, a total of 14 were known with human hosts.[4] However, some polyomaviruses are associated with human disease, particularly in immunocompromised individuals. MCV is highly divergent from the other human polyomaviruses and is most closely related to murine polyomavirus. Trichodysplasia spinulosa-associated polyomavirus (TSV) is distantly related to MCV. Two viruses—HPyV6 and HPyV7—are most closely related to KI and WU viruses, while HPyV9 is most closely related to the African green monkey-derived lymphotropic polyomavirus (LPV).[citation needed]

A fourteenth virus has been described.[44] Lyon IARC polyomavirus is related to raccoon polyomavirus.[citation needed]

List of human polyomaviruses

[edit]

The following 14 polyomaviruses with human hosts had been identified and had their genomes sequenced as of 2017:[4]

Species Proposed genus Virus name Abbreviation NCBI RefSeq Year of discovery Clinical correlate (if any) References
Human polyomavirus 5 Alpha Merkel cell polyomavirus MCPyV NC_010277 2008 Merkel cell cancer[5] [45][11][46]
Human polyomavirus 8 Alpha Trichodysplasia spinulosa polyomavirus TSPyV NC_014361 2010 Trichodysplasia spinulosa[5] [47][48]
Human polyomavirus 9 Alpha Human polyomavirus 9 HPyV9 NC_015150 2011 None known [49]
Human polyomavirus 12 Alpha Human polyomavirus 12 HPyV12 NC_020890 2013 None known [50]
Human polyomavirus 13 Alpha New Jersey polyomavirus NJPyV NC_024118 2014 None known [51]
Human polyomavirus 1 Beta BK polyomavirus BKPyV NC_001538 1971 Polyomavirus-associated nephropathy; haemorrhagic cystitis[5] [52]
Human polyomavirus 2 Beta JC polyomavirus JCPyV NC_001699 1971 Progressive multifocal leukoencephalopathy[5] [53]
Human polyomavirus 3 Beta KI polyomavirus KIPyV NC_009238 2007 None known [54]
Human polyomavirus 4 Beta WU polyomavirus WUPyV NC_009539 2007 None known [15]
Human polyomavirus 6 Delta Human polyomavirus 6 HPyV6 NC_014406 2010 HPyV6 associated pruritic and dyskeratotic dermatosis (H6PD)[55] [32]
Human polyomavirus 7 Delta Human polyomavirus 7 HPyV7 NC_014407 2010 HPyV7-related epithelial hyperplasia[55][56][57] [32]
Human polyomavirus 10 Delta MW polyomavirus MWPyV NC_018102 2012 None known [58][59][60]
Human polyomavirus 11 Delta STL polyomavirus STLPyV NC_020106 2013 None known [61]
Human polyomavirus 14 Alpha Lyon IARC polyomavirus LIPyV NC_034253.1 2017 None known [62][63]

Deltapolyomavirus contains only the four human viruses shown in the above table. The Alpha and Beta groups contain viruses that infect a variety of mammals. The Gamma group contains the avian viruses.[4] Clinically significant disease associations are shown only where causality is expected.[5][64]

Antibodies to the monkey lymphotropic polyomavirus have been detected in humans suggesting that this virus - or a closely related virus - can infect humans.[65]

Clinical relevance

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All the polyomaviruses are highly common childhood and young adult infections.[66] Most of these infections appear to cause little or no symptoms. These viruses are probably lifelong persistent among almost all adults. Diseases caused by human polyomavirus infections are most common among immunocompromised people; disease associations include BK virus with nephropathy in renal transplant and non-renal solid organ transplant patients,[8][9] JC virus with progressive multifocal leukoencephalopathy,[10] and Merkel cell virus (MCV) with Merkel cell cancer.[11]

SV40

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Main article: SV40

SV40 replicates in the kidneys of monkeys without causing disease, but can cause cancer in rodents under laboratory conditions. In the 1950s and early 1960s, well over 100 million people may have been exposed to SV40 due to previously undetected SV40 contamination of polio vaccine, prompting concern about the possibility that the virus might cause disease in humans.[67][68] Although it has been reported as present in some human cancers, including brain tumors, bone tumors, mesotheliomas, and non-Hodgkin's lymphomas,[69] accurate detection is often confounded by high levels of cross-reactivity for SV40 with widespread human polyomaviruses.[68] Most virologists dismiss SV40 as a cause for human cancers.[67][70][71]

Diagnosis

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The diagnosis of polyomavirus almost always occurs after the primary infection as it is either asymptomatic or sub-clinical. Antibody assays are commonly used to detect presence of antibodies against individual viruses.[72] Competition assays are frequently needed to distinguish among highly similar polyomaviruses.[73]

In cases of progressive multifocal leucoencephalopathy (PML), a cross-reactive antibody to SV40 T antigen (commonly Pab419) is used to stain tissues directly for the presence of JC virus T antigen. PCR can be used on a biopsy of the tissue or cerebrospinal fluid to amplify the polyomavirus DNA. This allows not only the detection of polyomavirus but also which sub type it is.[74]

There are three main diagnostic techniques used for the diagnosis of the reactivation of polyomavirus in polyomavirus nephropathy (PVN): urine cytology, quantification of the viral load in both urine and blood, and a renal biopsy.[72] The reactivation of polyomavirus in the kidneys and urinary tract causes the shedding of infected cells, virions, and/or viral proteins in the urine. This allows urine cytology to examine these cells, which if there is polyomavirus inclusion of the nucleus, is diagnostic of infection.[75] Also as the urine of an infected individual will contain virions and/or viral DNA, quantitation of the viral load can be done through PCR.[76] This is also true for the blood.

Renal biopsy can also be used if the two methods just described are inconclusive or if the specific viral load for the renal tissue is desired. Similarly to the urine cytology, the renal cells are examined under light microscopy for polyomavirus inclusion of the nucleus, as well as cell lysis and viral partials in the extra cellular fluid. The viral load as before is also measure by PCR.[citation needed]

Tissue staining using a monoclonal antibody against MCV T antigen shows utility in differentiating Merkel cell carcinoma from other small, round cell tumors.[77] Blood tests to detect MCV antibodies have been developed and show that infection with the virus is widespread although Merkel cell carcinoma patients have exceptionally higher antibody responses than asymptomatically infected persons.[7][78][79][80]

Use in tracing human migration

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The JC virus offers a promising genetic marker for human evolution and migration.[81][82] It is carried by 70–90 percent of humans and is usually transmitted from parents to offspring. This method does not appear to be reliable for tracing the recent African origin of modern humans.[citation needed]

History

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Murine polyomavirus was the first polyomavirus discovered, having been reported by Ludwik Gross in 1953 as an extract of mouse leukemias capable of inducing parotid gland tumors.[83] The causative agent was identified as a virus by Sarah Stewart and Bernice Eddy, after whom it was once called "SE polyoma".[84][85][86] The term "polyoma" refers to the viruses' ability to produce multiple (poly-) tumors (-oma) under certain conditions. The name has been criticized as a "meatless linguistic sandwich" ("meatless" because both morphemes in "polyoma" are affixes) giving little insight into the viruses' biology; in fact, subsequent research has found that most polyomaviruses rarely cause clinically significant disease in their host organisms under natural conditions.[87]

Dozens of polyomaviruses have been identified and sequenced as of 2017, infecting mainly birds and mammals. Two polyomaviruses are known to infect fish, the black sea bass[88] and gilthead seabream.[89] A total of fourteen polyomaviruses are known to infect humans.[4]

References

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Polyomaviridae

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The Polyomaviridae is a family of small, non-enveloped viruses with icosahedral symmetry and circular double-stranded DNA genomes of approximately 5,000 base pairs, which establish persistent infections in a wide range of hosts including mammals, birds, and fish. These viruses are notable for their oncogenic potential, particularly in immunocompromised individuals, where they can cause diseases such as nephropathy, encephalitis, and certain cancers through mechanisms involving disruption of host cell cycle regulation. Taxonomically, the Polyomaviridae belongs to the realm Monodnaviria, kingdom Shotokuvirae, phylum Cossaviricota, class Papovaviricetes, and order Sepolyvirales, and currently encompasses eight genera—Alphapolyomavirus, Betapolyomavirus, Deltapolyomavirus, Epsilonpolyomavirus, Etapolyomavirus, Gammapolyomavirus, Thetapolyomavirus, and Zetapolyomavirus—with 122 recognized species (as of 2025) distributed across these genera or unassigned. Virions measure 40–45 nm in diameter, exhibit T=7dextro icosahedral symmetry, and are composed primarily of the major capsid protein VP1 (forming 72 pentameric capsomers), along with minor proteins VP2 and VP3, while the genome is packaged with cellular histones. The genome organization features a non-coding control region (NCCR) containing the origin of replication, flanked by early and late transcription units; early genes encode regulatory proteins such as the large T antigen (LTAg) and small t antigen (STAg), while late genes produce the capsid proteins via alternative splicing. Replication occurs exclusively in the host cell nucleus through a bidirectional theta mechanism initiated at the unique origin within the NCCR, with LTAg playing a central role in unwinding DNA and recruiting host replication machinery. In humans, 14 polyomaviruses have been identified, primarily within the genera Alphapolyomavirus and Betapolyomavirus, including notable pathogens such as BK polyomavirus (BKPyV), JC polyomavirus (JCPyV), KI polyomavirus (KIPyV), WU polyomavirus (WUPyV), and Merkel cell polyomavirus (MCPyV). These viruses typically cause asymptomatic primary infections in childhood but can reactivate in immunosuppressed patients, leading to conditions like BKPyV-associated nephropathy and hemorrhagic cystitis in transplant recipients, JCPyV-induced progressive multifocal leukoencephalopathy in AIDS or transplant patients, trichodysplasia spinulosa from trichodysplasia spinulosa polyomavirus (TSPyV), and Merkel cell carcinoma from MCPyV. Veterinary significance includes oncogenic transformations in animal models, such as those induced by simian virus 40 (SV40), highlighting the family's broader role in tumor biology research.

Taxonomy

Genera

The family Polyomaviridae is currently classified into eight genera by the International Committee on Taxonomy of Viruses (ICTV) as of 2025: Alphapolyomavirus, Betapolyomavirus, Gammapolyomavirus, Deltapolyomavirus, Epsilonpolyomavirus, Zetapolyomavirus, Etapolyomavirus, and Thetapolyomavirus. These genera reflect phylogenetic relationships derived primarily from amino acid sequences of the large T antigen (LTAg), with delineation based on significant genetic divergence, typically exceeding 15% in LTAg amino acid identity, alongside shared genome organization and host specificity. Host associations further define these groupings, with most genera restricted to mammals, one to birds, and two to fish hosts. Mammalian genera include Alphapolyomavirus, which primarily infects rodents and primates, encompassing viruses like murine polyomavirus and some human-associated ones such as Merkel cell polyomavirus; Betapolyomavirus, associated with primates and including human pathogens like BK polyomavirus and JC polyomavirus; Deltapolyomavirus, linked to humans and other mammals with skin tropism, such as human polyomavirus 6; Epsilonpolyomavirus, infecting cetartiodactyls like cattle (e.g., bovine polyomavirus 1); and Zetapolyomavirus, specific to cetaceans such as dolphins (e.g., dolphin polyomavirus 1). Gammapolyomavirus is avian-specific, infecting birds like budgerigars and causing subclinical or severe infections without known oncogenicity. In contrast, Etapolyomavirus and Thetapolyomavirus represent fish-associated polyomaviruses, with examples like giant guitarfish polyomavirus in Etapolyomavirus, expanding the family's host range beyond terrestrial vertebrates. These host-specific patterns underscore the family's evolutionary co-speciation with vertebrate lineages. Taxonomic evolution within Polyomaviridae began with a single genus, Polyomavirus, but the ICTV restructured it in 2011 into three initial genera—Orthopolyomavirus and Wukipolyomavirus for mammals, and Avipolyomavirus for birds—based on LTAg phylogeny and host range. Subsequent discoveries of diverse polyomaviruses led to further refinements: by 2016, four genera (Alpha-, Beta-, Gamma-, and Deltapolyomavirus) were established, incorporating genetic thresholds and genomic features like intron presence in LTAg coding sequences. The addition of Epsilonpolyomavirus and Zetapolyomavirus in 2020 addressed mammalian diversity, while 2021 proposals created Etapolyomavirus and Thetapolyomavirus to accommodate fish viruses, renaming all species to binomial format and reaching eight genera by 2022. This progression reflects ongoing ICTV efforts to integrate metagenomic data and phylogenetic analyses for robust classification.

Species classification

The family Polyomaviridae comprises 118 species, nearly all assigned to the eight genera—Alphapolyomavirus, Betapolyomavirus, Deltapolyomavirus, Epsilonpolyomavirus, Gammapolyomavirus, Zetapolyomavirus, Etapolyomavirus, and Thetapolyomavirus—as of 2025. Species classification within these genera is determined primarily through phylogenetic analysis of the large T antigen amino acid sequence, with demarcation requiring greater than 15% divergence from the nearest relative. Notable examples include Mus musculus polyomavirus 1 (formerly murine polyomavirus) in the genus Alphapolyomavirus, which primarily infects rodents, and Macaca mulatta polyomavirus 1 (simian virus 40, or SV40) in Betapolyomavirus, associated with primate hosts. Naming conventions for polyomavirus species are typically host-derived, incorporating the host genus or common name followed by "polyomavirus" and a numerical suffix for distinct variants, such as BK polyomavirus (BKPyV) for a human-infecting species in Betapolyomavirus. Newly discovered species often receive provisional designations pending full genomic characterization and ICTV ratification, reflecting the rapid expansion driven by metagenomic surveillance. The family's species exhibit substantial host diversity, with approximately 14 species infecting humans (distributed across Alphapolyomavirus, Betapolyomavirus, and Deltapolyomavirus), more than 70 infecting other mammals (predominantly in Alphapolyomavirus and Betapolyomavirus), over 10 avian species (mainly in Gammapolyomavirus), and an emerging group in fish hosts (such as Rhynchobatus djiddensis polyomavirus 1 in Etapolyomavirus). Post-2020 discoveries, including additional fish polyomaviruses identified through metagenomic sequencing (e.g., a novel species in the thornback skate Raja clavata), have further highlighted the expanding scope of polyomavirus host range beyond traditional mammalian and avian reservoirs.

Structure and genome

Virion morphology

The virions of the Polyomaviridae family are non-enveloped viruses featuring an icosahedral capsid with T=7d quasi-symmetry and a diameter ranging from 40 to 50 nm. This compact structure encapsulates the circular double-stranded DNA genome, enabling efficient transmission and persistence in various hosts. The capsid is primarily assembled from 72 pentameric units of the major capsid protein VP1, totaling 360 copies that form the outer shell through pentavalent and hexavalent interactions stabilized by calcium ions and C-terminal arms. Minor capsid proteins VP2 and VP3, present in approximately 1 copy per pentamer, are embedded on the inner surface, contributing to genome packaging and structural integrity without altering the external morphology. Under electron microscopy, polyomavirus virions appear as smooth, spherical particles lacking surface spikes, tails, or other projections, with a uniform isometric outline resolved at resolutions up to 7.6 Å via cryo-electron microscopy. This featureless exterior facilitates receptor binding and environmental survival. Polyomavirus virions exhibit remarkable stability, resisting heat, detergents, low pH, and other environmental stresses, which supports their persistence outside hosts and potential fecal-oral transmission routes.90205-0)

Genome organization and features

The genomes of polyomaviruses are non-segmented, circular, double-stranded DNA molecules typically ranging from 3,962 to 7,369 base pairs in length, with most around 5,000 base pairs. In the mature virion, the genome adopts a supercoiled topology and is organized as a minichromosome complexed with host cellular histones H2A, H2B, H3, and H4. The guanine-cytosine (GC) content varies between 40% and 50%, contributing to the compact nature of the genome. The genome is divided into three main regions: an early coding region, a late coding region, and a non-coding control region (NCCR) that separates them. The NCCR, which constitutes about 10% of the genome, is highly conserved in core elements but hypervariable in sequence and architecture across species; it contains the origin of replication, bidirectional promoters, and enhancer sequences that regulate transcription of both early and late genes. Rearrangements or duplications in the NCCR, as observed in human polyomaviruses like BKPyV and JCPyV, are associated with altered transcriptional activity and increased pathogenicity. The early region encodes open reading frames (ORFs) for the large T antigen (LTAg) and small T antigen (STAg), transcribed in the direction opposite to the late region. The late region contains ORFs for the major capsid protein VP1, minor capsid proteins VP2 and VP3 (sharing a common start but with alternative initiation), and in some species, an agnoprotein. Additionally, microRNA genes are encoded within the late region archetype, often overlapping the LTAg ORF in an antisense orientation. Polyomavirus genomes are generally compact and intron-free, with continuous ORFs in the coding regions, though exceptions exist such as two introns in the LTAg ORF of epsilonpolyomaviruses. This organization enables efficient packing and bidirectional gene expression from a single promoter system.

Replication cycle

Viral entry and uncoating

Polyomaviruses initiate infection through receptor-mediated attachment at the cell surface, primarily involving the major capsid protein VP1, which binds to sialic acid-containing glycans. For instance, simian virus 40 (SV40) attaches to the ganglioside GM1 via its VP1 pentamer, while JC polyomavirus (JCV) interacts with GT1b gangliosides or the lactoseries tetrasaccharide c (LSTc) structure terminating in α2,6-linked sialic acid. Similarly, BK polyomavirus (BKV) employs GT1b or α2,3-linked sialic acid on gangliosides, and Merkel cell polyomavirus (MCPyV) recognizes sialylated glycosaminoglycans and GT1b as co-receptors. These interactions are critical for species and tissue specificity, as receptor distribution influences host range and tropism; for example, LSTc expression on glial cells restricts JCV to neural tissues. Following attachment, polyomaviruses enter host cells via endocytosis, with pathways varying by virus. SV40 and BKV typically utilize caveolin-mediated endocytosis (Cav-ME) through lipid rafts, independent of clathrin and dynamin, while JCV employs clathrin-mediated endocytosis (CME) involving the serotonin receptor 5-HT2AR and β-arrestin. MCPyV also follows Cav-ME, often via ganglioside clustering in caveolae. Internalized virions traffic along microtubules using dynein motors to early endosomes and then to the endoplasmic reticulum (ER), a process facilitated by COPI vesicles for SV40 and JCV, or ganglioside GD1a sorting for BKV and mouse polyomavirus. This ER targeting is a hallmark of polyomavirus entry, distinguishing it from endosomal uncoating in many other non-enveloped viruses. Uncoating occurs primarily in the ER, where host redox enzymes trigger capsid disassembly. ER-resident protein disulfide isomerases (PDIs), such as PDI and ERp29, reduce inter-pentameric disulfide bonds in VP1, inducing conformational changes that expose hydrophobic regions and the minor proteins VP2/VP3. This facilitates partial disassembly and engagement with the ER-associated degradation (ERAD) machinery, including derlin proteins and the chaperone BiP, which translocate the virion to the cytosol. In the cytosol, further disassembly under reducing conditions and low calcium exposes nuclear localization signals (NLS) on VP2/VP3, enabling importin-mediated transport of the viral genome or subviral particles into the nucleus via nuclear pore complexes. For SV40, this process requires Hsc70 and associated chaperones for complete uncoating, ensuring genome release without full capsid rupture at the plasma membrane. Receptor specificity and ER trafficking efficiency thus serve as key determinants of productive infection across Polyomaviridae.

Gene expression and replication

Upon entry into the host cell nucleus, the polyomavirus genome initiates the early phase of gene expression through bidirectional transcription controlled by the noncoding control region (NCCR). The NCCR contains promoter and enhancer elements that drive transcription of the early region from one strand, producing primary transcripts that are differentially spliced to yield mRNAs encoding the large T antigen (LTAg) and small T antigen (STAg). These early proteins are translated in the cytoplasm, with LTAg playing a central role in subsequent viral processes by binding back to the NCCR to autoregulate transcription. Viral DNA replication begins at the origin within the NCCR, where LTAg binds to specific GAGGC pentanucleotide repeats via its origin-binding domain, forming a double hexamer that acts as an ATP-dependent helicase to unwind the DNA bidirectionally. This unwinding recruits host cell replication factors, including DNA polymerase α-primase and replication protein A (RPA), which synthesize new viral DNA strands using the host machinery, as polyomaviruses lack their own polymerase. Replication proceeds in a bidirectional theta mode, generating displaced single-stranded DNA templates that support further amplification of the circular genome. Recent proteomic analyses have profiled host proteins at these nuclear replication centers, revealing key interactions with cellular factors beyond the core replication proteins. The transition to the late phase occurs after the onset of genome replication, with amplification of viral DNA templates triggering increased transcription of late genes from the opposite strand of the NCCR. This switch involves enhanced late mRNA stability and processing, including inefficient polyadenylation that allows readthrough transcription to produce multigenomic late transcripts, which are then spliced into mature mRNAs encoding capsid proteins; the precise molecular trigger remains incompletely understood but is linked to the accumulation of replicated genomes diluting early repressors. Concurrently, late-strand transcription generates antisense RNAs that form double-stranded structures with early mRNAs, leading to A-to-I editing by host ADAR enzymes, which promotes nuclear retention and degradation of early transcripts. Regulation of these processes ensures efficient replication while modulating host responses; LTAg binds tumor suppressors such as p53 and Rb family proteins, inactivating p53 to prevent apoptosis and sequestering Rb to release E2F transcription factors, which classically drives host cells into S phase (as in SV40) to provide replication factors; however, recent studies on BK polyomavirus indicate that LTAg expression itself is enhanced following initial host S phase entry. Additionally, polyomaviruses encode microRNAs (miRNAs) from the late strand that target early region mRNAs, cleaving or repressing LTAg and STAg translation to autoregulate replication levels and limit immune detection during persistent infection. For instance, in BK polyomavirus, miRNA-mediated suppression of LTAg reduces excessive genome amplification, contributing to viral latency.

Assembly and egress

Assembly of polyomavirions occurs in the nucleus of infected host cells, where the major capsid protein VP1 self-assembles into pentamers that form the outer shell of the icosahedral capsid. These VP1 pentamers encapsulate the replicated viral DNA, which is organized into a chromatin-like structure by association with host cell histones H2A, H2B, H3, and H4, facilitating packaging and stabilization during maturation. The minor capsid proteins VP2 and VP3, which share a common N-terminal region but differ in their C-termini due to alternative splicing, bind within the central cavity of each VP1 pentamer, contributing to DNA packaging and internal scaffolding of the virion. Additionally, the agnoprotein, a small late-expressed protein, aids in the efficient packaging of the viral genome into assembling capsids by interacting with capsid components and modulating nuclear egress pathways. Virion maturation involves the completion of capsid formation around the histone-associated minichromosome, resulting in stable, non-enveloped icosahedral particles approximately 40-50 nm in diameter. In productive infections, this process yields 500-1000 infectious virions per cell, depending on the host cell type and viral strain, such as in simian virus 40 (SV40) infections of permissive monkey cells. The assembled capsids accumulate in the nucleus before egress. Egress of polyomavirions from infected cells can occur through both lytic and non-lytic mechanisms. In lytic infections, cell lysis releases virions, leading to host cell death and spread to neighboring cells. However, many polyomaviruses, including BK polyomavirus (BKPyV), primarily employ non-lytic release, where virions traffic through the endoplasmic reticulum (ER) and Golgi apparatus or are packaged into extracellular vesicles for exocytosis, allowing persistent infection without immediate cytotoxicity. In some cases, such as with BKPyV, virions hijack host extracellular vesicles, which may acquire a lipid envelope, facilitating en bloc transmission and immune evasion. The agnoprotein plays a critical role in this non-lytic egress by disrupting cellular membranes and promoting virion release without lysing the cell.

Viral proteins

Early proteins (T antigens)

The early proteins of polyomaviruses, expressed during the initial phase of infection from the early region of the viral genome, primarily consist of the large T antigen (LTAg) and small t antigen (STAg), which are essential for initiating viral DNA replication and modulating host cell processes. These proteins are transcribed from a common precursor mRNA that undergoes alternative splicing to produce the distinct isoforms, with expression occurring shortly after viral entry and preceding late gene activation. LTAg is a multifunctional protein, typically ranging from 641 to 817 amino acids in length, featuring several key domains that enable its diverse roles. The N-terminal J-domain, approximately 70 residues long, facilitates interactions with host chaperones like Hsc70, while an intrinsically disordered region (IDR) contains motifs such as LXCXE for binding retinoblastoma (Rb) family proteins, followed by a TPPK nuclear localization signal (NLS). The central origin-binding domain (OBD) recognizes specific GAGGC pentanucleotide sequences in the viral origin of replication, and the C-terminal helicase domain includes ATPase and zinc-binding motifs that drive DNA unwinding. As a replicative helicase, LTAg forms hexameric complexes to unwind double-stranded DNA, recruit cellular replication factors like RPA and DNA polymerase α-primase, and initiate bidirectional DNA synthesis, making it indispensable for viral genome amplification. Additionally, LTAg promotes cell immortalization by binding and inactivating tumor suppressors: it interacts with p53 via its C-terminal region to prevent transcriptional activation and apoptosis, and with Rb via the LXCXE motif to release E2F transcription factors, thereby driving cell cycle progression into S phase. Some polyomaviruses, such as those in the SV40 class (e.g., BKPyV, JCV), include a variable host range (VHR) domain at the C-terminus that modulates species-specific replication efficiency. STAg, a shorter isoform sharing the N-terminal J-domain and IDR with LTAg but lacking the OBD and helicase domains, plays a supportive role in replication and cellular transformation. It binds directly to the protein phosphatase 2A (PP2A) holoenzyme, particularly the A and C subunits, thereby inhibiting PP2A's dephosphorylation activity and disrupting its regulation of signaling pathways. This interaction activates the mitogen-activated protein kinase (MAPK) pathway by preventing dephosphorylation of key components like MEK1/2 and ERK1/2, leading to sustained phosphorylation of downstream targets such as c-Jun and enhanced cell proliferation. In human polyomaviruses like BKPyV and MCPyV, STAg's PP2A binding further influences viral gene expression and DNA replication efficiency, often synergizing with LTAg to promote oncogenesis. Alternative splicing variants expand the early proteome; for instance, Merkel cell polyomavirus (MCPyV) produces a 57kT antigen that retains Rb-binding capability but exhibits distinct regulatory functions, while mouse polyomavirus encodes a middle T antigen (MTAg) with a unique C-terminal region containing cysteine repeats for membrane association and activation of signaling cascades akin to growth factor receptors. These variants, expressed in the early phase, are critical for species-specific pathogenesis and transformation.

Late proteins (capsid and accessory)

The late phase of the polyomavirus replication cycle produces structural proteins that form the viral capsid and accessory proteins that facilitate virion maturation and release. These proteins are encoded by the late region of the genome, transcribed from the viral non-coding control region following the initiation of DNA replication. VP1 is the major capsid protein, comprising approximately 80% of the virion mass and forming the outer shell of the icosahedral capsid. It self-assembles into 72 pentamers arranged in a T=7d symmetry, with each pentamer consisting of five VP1 monomers that interlock via β-strands and loops to create a stable structure approximately 85 Å in diameter and 40 Å high. The VP1 pentamers are linked by calcium ions at inter-pentamer interfaces, which stabilize the capsid against disassembly during entry, and feature prominent BC and HI loops on the exterior surface that mediate receptor binding to sialylated glycans such as GT1b or GD1b. The N-terminal arm of VP1 extends inward to interact with the viral genome, aiding in DNA packaging. VP2 and VP3 are minor internal capsid proteins that share a common C-terminal domain but differ in length due to alternative translation initiation: VP2 is longer (approximately 351 amino acids in BK polyomavirus) and includes an N-terminal extension absent in VP3. Both proteins insert into the central pore of VP1 pentamers as α-helical hairpins, occupying density within the capsid interior and contributing to less than 20% of the total protein content. They contain nuclear localization signals (NLS) and DNA-binding motifs, enabling the transport of incoming capsids to the nucleus and potentially serving as internal scaffolds during assembly, though capsids formed solely from VP1 retain near-normal morphology. Absence of VP2 and VP3 reduces infectivity by over 99%, underscoring their essential role in genome delivery. Agnoprotein is a small accessory protein (typically 60-70 amino acids in mammalian polyomaviruses like BK and JC viruses) that localizes to the perinuclear region, cytoplasm, and membranes, forming dimers and oligomers via a central hydrophobic α-helix. It associates with lipid droplets and the endoplasmic reticulum through residues such as 20-42 in BK polyomavirus, functioning as a viroporin to disrupt membrane integrity and promote ion flux. Agnoprotein facilitates virion egress by interacting with proteins like FEZ1 and α-SNAP, inhibiting host secretion pathways and enhancing nuclear export of capsids; it also aids in DNA release from the capsid during uncoating, though it is dispensable for replication in some cell types. Phosphorylation at sites like Ser-11 modulates its activity, and it downregulates DNA replication by binding PCNA. This protein is absent in some polyomaviruses, such as Merkel cell and KI polyomaviruses, indicating it is not universal across the family. In avian polyomaviruses, the agnoprotein homolog is designated VP4, a minor structural protein incorporated into virions that induces host cell apoptosis to promote viral spread and may assist in genome packaging. Some polyomavirus accessory proteins, including agnoprotein, exhibit viroporin activity to permeabilize membranes during egress.

Human polyomaviruses

List of known human polyomaviruses

As of 2025, 14 human polyomaviruses have been identified within the family Polyomaviridae, classified into the genera Alphapolyomavirus, Betapolyomavirus, and Deltapolyomavirus. These viruses establish persistent infections in humans, often asymptomatically, and are detected across various tissues and body fluids. The discovery of these polyomaviruses spans over five decades, beginning with traditional virus isolation from clinical specimens and evolving to modern techniques like polymerase chain reaction (PCR) and metagenomic sequencing for identifying novel species in asymptomatic or environmental samples. For instance, early detections relied on cell culture propagation from urine or contaminated vaccines, while recent isolates frequently emerge from deep sequencing of skin swabs, respiratory secretions, or stool. Human polyomaviruses exhibit high prevalence worldwide, with seropositivity rates often surpassing 80% for established species like BKPyV and JCPyV among adults, reflecting early childhood acquisition and lifelong persistence. Less common ones show variable seroprevalence, typically 30-70%, depending on detection methods and populations studied.
Virus NameDiscovery YearPrimary SourceGenus
JC polyomavirus (JCPyV)1971Urine (PML patient)Betapolyomavirus
BK polyomavirus (BKPyV)1971Urine (transplant patient)Betapolyomavirus
KI polyomavirus (KIPyV)2007Respiratory secretionsBetapolyomavirus
WU polyomavirus (WUPyV)2007Respiratory secretionsBetapolyomavirus
Merkel cell polyomavirus (MCPyV)2008Skin (Merkel cell carcinoma)Alphapolyomavirus
Human polyomavirus 6 (HPyV6)2010SkinDeltapolyomavirus
Human polyomavirus 7 (HPyV7)2010SkinDeltapolyomavirus
Trichodysplasia spinulosa polyomavirus (TSPyV)2010SkinAlphapolyomavirus
Human polyomavirus 9 (HPyV9)2011SerumAlphapolyomavirus
Human polyomavirus 10 (HPyV10, MWPyV, Malawi polyomavirus)2012StoolDeltapolyomavirus
STL polyomavirus (STLPyV, HPyV11)2013StoolDeltapolyomavirus
Human polyomavirus 12 (HPyV12)2013SkinAlphapolyomavirus
New Jersey polyomavirus (NJPyV, HPyV13)2014SkinAlphapolyomavirus
Lyon IARC polyomavirus (LIPyV, HPyV14)2017SkinAlphapolyomavirus

Pathogenesis and clinical manifestations

Human polyomaviruses typically establish persistent, asymptomatic infections in immunocompetent individuals following primary acquisition during early childhood. These viruses remain latent in various tissues, such as the kidneys, bone marrow, or skin, and rarely cause disease unless reactivation occurs in the setting of immunosuppression, including HIV/AIDS, organ transplantation, or pharmacologic immunosuppression. Transmission primarily happens through respiratory routes via aerosols or secretions, as well as fecal-oral or urine-oral pathways, with evidence of early childhood seroconversion rates exceeding 50-90% for major types like JCPyV and BKPyV. Sexual transmission has also been implicated for some, such as BKPyV in adults. JC polyomavirus (JCPyV) is the primary cause of progressive multifocal leukoencephalopathy (PML), a demyelinating disease of the central nervous system that manifests in severely immunocompromised patients. Pathogenesis involves viral reactivation from latency in renal tubular cells or bone marrow, followed by hematogenous spread to the brain, where JCPyV undergoes lytic infection of oligodendrocytes, leading to multifocal white matter lesions. Clinical features include progressive cognitive impairment, motor deficits, ataxia, visual disturbances, and personality changes, with an incidence of 3-5% in untreated HIV patients and poor prognosis without immune reconstitution. Rearrangements in the non-coding control region (NCCR) of the JCPyV genome enhance neurovirulence by promoting replication in glial cells and altering tropism from renal to neural tissues. BK polyomavirus (BKPyV) primarily affects the urinary tract, causing polyomavirus-associated nephropathy (PVAN) in 1-10% of kidney transplant recipients and hemorrhagic cystitis in 5-29% of hematopoietic stem cell transplant patients. Following reactivation from latency in uroepithelial cells, BKPyV replicates lytically in renal tubular epithelium and bladder urothelium, resulting in tubulointerstitial nephritis, tubular atrophy, interstitial fibrosis, and potential allograft loss in up to 50% of PVAN cases if untreated. Hemorrhagic cystitis presents with dysuria, hematuria, and urinary frequency, often peaking 2-3 months post-transplant due to high viral loads in urine exceeding 10^7 copies/mL. Risk factors include intense immunosuppression and BKPyV seropositivity in donors or recipients. Merkel cell polyomavirus (MCPyV) is strongly associated with Merkel cell carcinoma (MCC), an aggressive neuroendocrine skin cancer occurring predominantly in elderly or immunosuppressed individuals. Pathogenesis entails initial cutaneous infection leading to persistent viral presence in skin, followed by clonal integration of the mutated viral genome into host Merkel cells, where truncated large T antigen expression drives cell proliferation and inhibits tumor suppressors like p53 and Rb. Approximately 80% of MCC tumors harbor integrated MCPyV DNA, correlating with tumor development through chronic antigenic stimulation and immune evasion. Clinical manifestations include rapidly growing, painless dermal nodules on sun-exposed areas, with high recurrence rates and metastasis potential. Other human polyomaviruses, such as trichodysplasia spinulosa-associated polyomavirus (TSPyV), KI polyomavirus (KIPyV), and WU polyomavirus (WUPyV), are linked to rare manifestations primarily in immunocompromised hosts. TSPyV causes trichodysplasia spinulosa, a disfiguring follicular skin disease characterized by spiny, keratinized papules on the face and extremities, resulting from lytic replication in inner root sheath cells of hair follicles. KIPyV and WUPyV, acquired via respiratory transmission in early childhood, have been detected in nasopharyngeal aspirates of children with acute respiratory illness, though their role in pathogenesis remains unclear and likely opportunistic.

Diagnosis and management

Diagnosis of human polyomavirus infections primarily relies on molecular detection of viral DNA, with polymerase chain reaction (PCR) assays targeting specific polyomavirus genomes in clinical specimens such as urine, plasma, cerebrospinal fluid (CSF), or tissue biopsies. For BK polyomavirus (BKPyV), quantitative PCR (qPCR) in urine detects viruria, while plasma qPCR monitors viremia; viral loads exceeding 10,000 copies/mL in plasma are associated with increased risk of BKPyV-associated nephropathy in kidney transplant recipients. In cases of progressive multifocal leukoencephalopathy (PML) caused by JC polyomavirus (JCPyV), CSF qPCR for JCPyV DNA has a high positive predictive value (>95%) when combined with compatible clinical and radiographic findings, though sensitivity can be lower in early disease due to low viral loads. Serological assays, such as enzyme-linked immunosorbent assays (ELISAs) for anti-polyomavirus antibodies (e.g., against VP1 capsid protein), help assess prior exposure and distinguish primary infection from reactivation, with seroprevalence rates for BKPyV and JCPyV exceeding 80% in adults. For Merkel cell polyomavirus (MCPyV)-associated Merkel cell carcinoma (MCC), diagnosis involves histopathological examination of skin biopsies, where immunohistochemistry (IHC) detects MCPyV large T antigen expression in over 80% of cases, often alongside cytokeratin-20 positivity to confirm MCC. Imaging modalities support diagnosis and monitoring: magnetic resonance imaging (MRI) reveals characteristic multifocal white matter lesions without mass effect or enhancement in PML, aiding presumptive diagnosis when CSF PCR is negative. For BKPyV nephropathy, renal ultrasound identifies allograft abnormalities like edema or hydronephrosis, while biopsy with IHC for SV40 large T antigen (cross-reactive with polyomaviruses) confirms tissue invasion. Management of polyomavirus-associated diseases focuses on reducing immunosuppression to restore immune control, as no specific antiviral therapies are universally approved. In BKPyV nephropathy, guidelines recommend decreasing calcineurin inhibitor doses or switching to alternative regimens upon detection of sustained viremia, which resolves infection in up to 90% of cases without allograft loss if initiated early. For PML, similar immunosuppression reduction is first-line, with adjunctive therapies like plasma exchange in natalizumab-associated cases to remove free JC virus antibody index; outcomes improve with immune reconstitution, though mortality remains 20-30%. Experimental antivirals include low-dose cidofovir (0.25-1 mg/kg every 1-3 weeks), which shows partial viral load reduction in BKPyV cases but lacks proven efficacy in randomized trials and carries nephrotoxicity risks; brivudine has been explored for JCPyV in vitro but not advanced clinically. No licensed vaccines exist for human polyomaviruses, though investigational virus-like particle (VLP) vaccines targeting JCPyV VP1 have demonstrated neutralizing antibody responses in preclinical models and phase I trials for high-risk patients. Post-transplant monitoring protocols are essential for early detection, particularly in kidney recipients where BKPyV reactivation peaks in the first year. The Kidney Disease: Improving Global Outcomes (KDIGO) guidelines advocate monthly plasma qPCR screening for BKPyV DNAemia for the first 3-6 months post-transplant, then quarterly up to one year, with urine cytology or decoy cell detection as a non-invasive initial screen; viruria prompts plasma testing to predict nephropathy risk. Challenges in diagnosis include differentiating reactivation (common in immunocompromised hosts) from primary infection, as serology indicates endemic exposure while PCR quantifies active replication; false-negative CSF PCR in early PML (up to 30% of cases) may necessitate brain biopsy for definitive diagnosis.

Non-human polyomaviruses

Animal polyomaviruses

Animal polyomaviruses infect a variety of non-human mammalian hosts, establishing persistent infections that are typically asymptomatic in adults but can lead to disease in neonates or immunocompromised individuals. These viruses serve as valuable models for understanding polyomavirus biology, oncogenesis, and pathogenesis due to their genetic similarities to human counterparts. In rodents, murine polyomavirus (MPyV), also known as mouse polyomavirus, is a well-studied alphapolyomavirus that naturally infects laboratory and wild mice, causing acute infections in newborns that can progress to tumors in multiple tissues, including salivary glands, kidneys, and skin. MPyV inoculation in neonatal mice induces oncogenic transformation through expression of its large T antigen, which disrupts host cell cycle regulation, making it a seminal model for studying viral oncogenesis mechanisms. In primates, simian virus 40 (SV40) is endemic to rhesus macaques (Macaca mulatta), where it causes subclinical infections in the respiratory and gastrointestinal tracts. Discovered in 1960 as a contaminant in polio vaccines produced using rhesus monkey kidney cells, SV40 led to widespread accidental exposure in humans via inactivated and oral vaccines administered between 1955 and 1963, with an estimated 10 to 30 million individuals in the United States exposed. In its natural host, SV40 persists latently without causing overt disease, though it can transform cells in vitro and induce tumors in experimentally infected rodents. Bovine polyomavirus (BPyV), classified in the genus Epsilonpolyomavirus, is commonly detected in cattle populations worldwide, often resulting in asymptomatic infections that establish lifelong persistence. Primary infection typically occurs early in life via fecal-oral transmission, with viral shedding in urine and feces, but clinical manifestations are rare in healthy animals. Polyomaviruses have also been identified in other mammals, including canines, equines, and bats, though their zoonotic potential remains low due to host specificity and limited cross-species transmission. Canine polyomavirus 1 (DogPyV-1), a betapolyomavirus, was first sequenced in 2017 from respiratory secretions of dogs with severe pneumonia, suggesting a possible role in respiratory disease, but its prevalence and pathogenicity require further study. In equines, equine polyomavirus (EPyV), isolated from healthy horses, shares genomic features with human Merkel cell polyomavirus and has been associated with rare cases of tubulointerstitial nephritis featuring tubular necrosis. Bats harbor a diverse array of polyomaviruses across multiple genera, with evidence of occasional host-switching within bat species, but inter-order transmission to other mammals is infrequent. These animal polyomaviruses provide critical research utility as models for human polyomavirus infections, particularly in studying progressive multifocal leukoencephalopathy (PML). MPyV, for instance, replicates productively in the central nervous system of immunodeficient mice, recapitulating demyelination and gliosis akin to JCPyV-induced PML, and has been used to evaluate antiviral therapies and immune responses. Similarly, SV40 models have informed investigations into polyomavirus entry and oncoprotein functions, bridging gaps in human disease research.

Avian and fish polyomaviruses

Avian polyomaviruses belong to the genus Gammapolyomavirus within the family Polyomaviridae, with representative species such as budgerigar fledgling disease virus 1 (BFDV-1), which primarily affects psittacine birds including budgerigars, lovebirds, macaws, conures, and cockatoos. These viruses cause acute, highly fatal infections in fledglings and young birds, characterized by symptoms like lethargy, regurgitation, abdominal distention, subcutaneous hemorrhages, diarrhea, and sudden death, often with mortality rates exceeding 90% in affected nests. BFDV-1 was first identified in 1981 as a papovavirus but was reclassified into the Polyomaviridae family following taxonomic revisions that separated polyomaviruses from papillomaviruses based on genomic and phylogenetic distinctions. Unlike mammalian polyomaviruses, which often establish persistent infections, avian polyomaviruses exhibit multipathogenic behavior and broad host tropism within psittacines, leading to rapid viral dissemination and tissue damage in multiple organs such as the liver, kidney, and spleen. This suggests adaptations for efficient replication in avian hosts, enabling acute disease progression within days of infection. Fish polyomaviruses represent divergent evolutionary lineages distinct from those infecting tetrapods, discovered primarily through metagenomic sequencing of environmental and tissue samples. Key examples include viruses detected in aquacultured species like gilt-head sea bream (Sparus aurata), often in association with lymphocystis disease lesions. Other detections occur in wild and farmed fish such as black sea bass, golden shiner, and emerald notothen (Trematomus bernacchii) from Antarctic waters, as well as cartilaginous fish like the giant guitarfish and thornback skate (Raja clavata), with the latter yielding a compact 4,195 bp genome from spleen samples collected off Portugal in 2021. These viruses form two non-monophyletic clades: one comprising perciform teleosts and another linked to cartilaginous fish, featuring variations in the large T antigen such as the absence of the DnaJ domain in some lineages, which may influence replication efficiency. Although no polyomaviruses have been directly linked to carp (Cyprinus carpio), their presence in economically important aquaculture species raises concerns for potential impacts on fish health, including subclinical infections that could exacerbate disease in intensive farming settings. Post-2020 discoveries have expanded non-mammalian polyomavirus diversity, particularly in aquatic environments, with the 2023 identification of thornback skate polyomavirus 1 highlighting ongoing metagenomic efforts to uncover viruses in understudied fish hosts. Fish polyomaviruses in cold-water species, such as Antarctic notothens and benthic skates, demonstrate adaptation to low-temperature habitats through phylogenetic divergence and genomic stability in chilled ecosystems, though specific molecular mechanisms remain under investigation. These findings underscore the need for surveillance in aquaculture to mitigate emerging viral threats in non-mammalian vertebrates.

Oncogenic potential

Molecular mechanisms

Polyomaviruses induce oncogenesis primarily through the actions of their early proteins, particularly the large T antigen (LTAg) and small T antigen (STAg), which disrupt key cellular regulatory pathways to promote uncontrolled cell proliferation. In vitro studies have demonstrated that these viral proteins can transform rodent and human cells, while animal models, such as hamsters and transgenic mice expressing polyomavirus T antigens, develop tumors including sarcomas and lymphomas, highlighting the oncogenic potential across species. The LTAg plays a central role by binding to the retinoblastoma protein (Rb), thereby releasing the E2F transcription factor to drive cells into S-phase and facilitate viral DNA replication, which inadvertently promotes host cell proliferation. Additionally, LTAg interacts with p53, sequestering it and inhibiting its transcriptional activity to suppress apoptosis, allowing transformed cells to evade programmed cell death. These mechanisms are conserved across polyomaviruses, though variations exist; for instance, in Merkel cell polyomavirus (MCPyV), LTAg retains Rb-binding capability but exhibits reduced p53 interaction compared to simian virus 40 (SV40). The STAg contributes to oncogenesis by binding and inhibiting protein phosphatase 2A (PP2A), a negative regulator of signaling cascades, which leads to sustained activation of the PI3K/AKT and MAPK pathways that enhance cell survival, growth, and proliferation. This PP2A inhibition disrupts dephosphorylation of key substrates, amplifying mitogenic signals independent of LTAg in some models. Viral genome integration into the host chromosome can further drive tumorigenesis, as seen in MCPyV-associated Merkel cell carcinoma (MCC), where the integrated viral DNA expresses a truncated LTAg that lacks the C-terminal helicase domain but preserves the Rb-binding LXCXE motif, enabling persistent oncogenic signaling without viral replication. In contrast, a "hit-and-run" mechanism has been proposed for other polyomaviruses like BK virus, wherein initial viral infection initiates genomic instability and transformation, but the viral sequences are subsequently lost, leaving no detectable viral DNA in the resulting tumor. Polyomaviruses also encode microRNAs (miRNAs) that contribute to oncogenesis by modulating host and viral gene expression to evade immune detection and promote cell survival. These viral miRNAs target early viral genes like LTAg to autoregulate replication and prevent lytic infection in transformed cells, while also downregulating host immune factors such as MHC class I molecules, thereby reducing antigen presentation and T-cell recognition. In mouse polyomavirus models, such miRNAs have been shown to enhance tumor persistence by inhibiting apoptosis-related pathways.

Associated cancers and examples

Merkel cell polyomavirus (MCPyV) is strongly associated with Merkel cell carcinoma (MCC), a rare and aggressive skin cancer, where the virus is detected in approximately 80% of cases through monoclonal integration of its DNA into the host genome. This integration typically involves truncations in the large T antigen, leading to persistent expression that drives oncogenesis, as evidenced by immunohistochemical detection of viral proteins in tumor cells. Epidemiological studies confirm that MCPyV-positive MCC tumors exhibit distinct clinical features, including higher rates in immunocompromised individuals, underscoring the virus's causal role. JC polyomavirus (JCPyV) has been implicated in brain tumors such as glioblastoma, though the association remains controversial and may involve mechanisms like antigenic cross-reactivity between viral T antigen and tumor proteins rather than direct transformation. Meta-analyses of human tumor samples show a significant correlation between JCPyV DNA presence and central nervous system malignancies, with pooled prevalence rates indicating higher detection in gliomas compared to controls. A 2025 study detected JCPyV DNA in 30.7% of pediatric brain tumors, with LTAg expression and activation of the Wnt/β-catenin pathway, suggesting a plausible mechanistic role in tumorigenesis. Additionally, JCPyV has been associated with upper tract urothelial carcinoma (UTUC), detected in 65.3% of cases in a 2025 Taiwanese cohort, correlating with increased odds of advanced disease progression (OR 9.13). However, prospective cohort studies have not consistently demonstrated increased glioma risk from JCPyV seropositivity, highlighting ongoing debates about causality. Simian virus 40 (SV40), a non-human polyomavirus, has been linked to human cancers including mesothelioma and osteosarcoma, primarily due to widespread exposure via contaminated polio vaccines administered between 1955 and 1963. Molecular evidence includes detection of SV40 DNA sequences and large T antigen expression in up to 60% of mesotheliomas and a subset of osteosarcomas, suggesting a contributory role in tumorigenesis. Despite this, large-scale epidemiological reviews, including those by the Institute of Medicine, conclude that the evidence is inadequate to establish definitive causality, as cancer incidence patterns post-exposure do not show clear elevations attributable to SV40. BK polyomavirus (BKPyV) is associated with urothelial carcinoma, particularly in immunocompromised patients such as kidney transplant recipients, where viral reactivation correlates with tumor development. Case series and matched studies report BKPyV DNA integration in 20-40% of post-transplant urothelial cancers, often with high viral loads indicating a potential oncogenic driver in this setting; a 2023 study found BKPyV in 21% of bladder cancers among solid organ transplant recipients. In contrast, associations are rare in immunocompetent individuals, emphasizing the role of immunosuppression in facilitating malignant transformation. In non-human models, mouse polyomavirus (MPyV) induces salivary gland tumors, including epitheliomas and adenocarcinomas, upon experimental inoculation in newborns, with tumors arising in 70-80% of cases and exhibiting viral DNA integration. These tumors provide insights into polyomavirus oncogenesis, as the virus targets epithelial cells leading to myoepitheliomas characteristic of parotid glands. Similarly, bovine polyomavirus (BPyV) demonstrates tumorigenic potential, including cell transformation assays that support associations with fibrosarcomas in experimental systems, though natural occurrences are less documented.

Evolutionary and epidemiological insights

Phylogenetic analysis

Phylogenetic analyses of the Polyomaviridae family primarily rely on sequences of the large T antigen (LTAg) and small T antigen (STAg) genes, which encode conserved proteins essential for viral replication and host interaction. These sequences reveal a tree-like structure where polyomaviruses cluster into distinct clades that largely mirror the phylogeny of their vertebrate hosts, supporting the co-speciation hypothesis. Under this model, polyomaviruses have evolved in parallel with their hosts over long timescales, with genera such as Alphapolyomavirus and Betapolyomavirus forming monophyletic groups aligned with mammalian orders. For instance, human polyomaviruses like BK and JC viruses cluster closely within the Betapolyomavirus genus, reflecting primate-specific divergence. This host-virus congruence is evident in co-phylogenetic reconciliation analyses, which identify significant codivergence events (e.g., up to 12 statistically significant events across mammalian polyomaviruses, P < 0.01), though some discrepancies suggest occasional deviations from strict co-speciation. Recombination events among polyomaviruses are rare, particularly in coding regions like LTAg and VP1, but have been detected in the non-coding control region (NCCR), which regulates viral gene expression and shows high variability. Ancient recombination signals are inferred from incongruent phylogenies between LTAg and capsid genes (e.g., VP1) in certain clades, such as avian and Wukipolyomavirus lineages, indicating historical gene exchanges that contributed to modern species diversity. In human pathogens like JC virus, NCCR rearrangements—often arising from intra-viral duplications or deletions rather than inter-viral recombination—alter transcriptional control and are associated with neurotropism, though these are not widespread across the family. Overall, the low recombination rate (no signals in VP1 alignments using tools like RDP4) underscores the predominance of vertical transmission in polyomavirus evolution. The family exhibits ancient origins, with divergence estimates placing the last common ancestor of polyomaviruses around 300–500 million years ago, coinciding with the radiation of bilaterian animals. This timeline is derived from molecular clock analyses calibrated against host fossil records, revealing a substitution rate of approximately 0.5% per million years in nucleotide sequences. Host jumps, while infrequent, have occurred, as exemplified by simian virus 40 (SV40), a Betapolyomavirus that jumped from rhesus macaques to humans via contaminated polio vaccines in the mid-20th century, leading to transient human infections without sustained transmission. Such events highlight exceptions to co-speciation, particularly in primates, but do not disrupt the overall host-specific pattern. Phylogenetic tools like maximum likelihood methods (e.g., PhyML) and Bayesian inference (e.g., BEAST, MrBayes) are routinely employed to construct trees and estimate genus boundaries, incorporating models of nucleotide substitution and divergence timing for robust inference.

Applications in population genetics

Polyomaviruses, particularly JC polyomavirus (JCPyV) and BK polyomavirus (BKPyV), serve as molecular markers in population genetics due to their persistent infection in humans and geographic structuring of genetic variants, reflecting ancient human dispersals. These viruses have co-evolved with human hosts over millennia, with subtype distributions aligning with major migratory events and supporting the Out-of-Africa model of human origins. By analyzing viral genomes from urine or blood samples across populations, researchers infer ancestry and migration routes without relying solely on human genetic data. JCPyV exhibits seven major genotypes (1, 2A–2D, 3, 4, 6–8) that correlate with distinct human ancestries: for example, genotype 1 with European origins, genotypes 2 with West Eurasian populations, genotype 3 with African Bantu, genotype 4 with South Asian, and genotypes 6–8 with indigenous African populations. This structuring has enabled mapping of historical migrations, such as the Bantu expansion in Africa, where Bantu populations carry admixed JCPyV profiles including African genotypes (3 and 6–8) from indigenous groups like Pygmies alongside European-influenced variants from later contacts. Methods like VP1 capsid protein sequencing, combined with phylogeographic modeling, reveal these patterns by constructing viral phylogenies overlaid on human demographic histories, while seroprevalence surveys (typically 70–90% globally) highlight uniform infection rates but genotype-specific prevalence tied to ethnicity. Similarly, BKPyV subtypes within genotype I show rearrangements and distributions that mirror migration routes, with subgroup Ib-2 predominant in European-descended populations and reflecting post-colonial dispersals to the Americas. Subgroup Ia prevails in African groups, Ib-1 in Southeast Asians, and Ic in Northeast Asians, indicating viral lineages that diverged alongside human movements out of Africa around 50,000–100,000 years ago. VP1 sequencing and seroprevalence patterns (80–90% in adults) further support this co-dispersal, providing evidence for multiple waves of human expansion and admixture. Overall, these viral markers underscore a long history of host-virus co-evolution, offering complementary insights into human population dynamics.

History

Initial discoveries

The discovery of the Polyomaviridae family began with the identification of the first member in mice. In 1953, Ludwik Gross isolated a filterable infectious agent from extracts of leukemic AKR mice that induced salivary gland carcinomas, specifically parotid tumors, in newborn C3H mice. This agent, later named murine polyomavirus, was characterized by its ability to cause multiple types of tumors in infected animals, leading to the coinage of the term "polyoma" to reflect its poly-tumorigenic properties. Early investigations confirmed its viral nature through serial passage in mice and initial electron microscopy observations revealing icosahedral particles approximately 40-50 nm in diameter. A significant advancement occurred in 1960 when simian virus 40 (SV40) was discovered as a contaminant in rhesus monkey kidney cell cultures used to produce poliovirus vaccines. Isolated by Benjamin Sweet and Maurice Hilleman, SV40 was identified through cytopathic effects, including vacuolization, in monkey cells and confirmed via electron microscopy showing non-enveloped, polyhedral virions. Further studies demonstrated its oncogenic potential: inoculation into newborn hamsters induced a variety of tumors, such as sarcomas and ependymomas, establishing SV40 as a model for viral oncogenesis and prompting widespread testing and removal from vaccine production by 1963. The 1960s and 1970s saw the recognition of human polyomaviruses. In 1965, John A. Zu Rhein and Steven M. Chou detected papovavirus-like particles via electron microscopy in brain tissue from a patient with progressive multifocal leukoencephalopathy (PML), linking the virus—later named JC polyomavirus (JCPyV)—to this demyelinating disease in immunocompromised individuals. Isolation followed in 1971. Meanwhile, that same year, Sylvia D. Gardner and colleagues isolated BK polyomavirus (BKPyV) from the urine of a renal transplant recipient experiencing ureteral stenosis, using electron microscopy and cell culture to confirm its presence as a novel human polyomavirus. These findings expanded the family to include human pathogens, initially studied through serological surveys and ultrastructural analysis.

Recent developments

Since the early 2000s, metagenomic approaches have dramatically expanded the known diversity of human polyomaviruses, identifying over 10 new types between 2007 and 2020. A landmark discovery was Merkel cell polyomavirus (MCPyV) in 2008, which was found to be clonally integrated in approximately 80% of Merkel cell carcinoma (MCC) tumors, establishing it as an etiological agent in this aggressive skin cancer. These findings, driven by high-throughput sequencing of clinical samples, have revealed widespread asymptomatic infections and highlighted the role of polyomaviruses in latent persistence within the human virome. Taxonomic classifications have evolved in parallel, with the International Committee on Taxonomy of Viruses (ICTV) expanding the Polyomaviridae family to eight genera—Alphapolyomavirus, Betapolyomavirus, Deltapolyomavirus, Etapolyomavirus, Epsilonpolyomavirus, Gammapolyomavirus, Thetapolyomavirus, and Zetapolyomavirus—by 2024, incorporating diverse mammalian, avian, and newly detected fish viruses. This update reflects the integration of genomic data from non-human hosts, including the first complete genome of a polyomavirus from a cartilaginous fish (Raja clavata polyomavirus 1) reported in 2023, broadening understanding of polyomavirus evolution across vertebrates. From 2021 to 2025, research has advanced functional characterization of polyomavirus accessory proteins, particularly agnoprotein, which modulates viral assembly, egress, and host cell responses in viruses like JC virus (JCV), BK virus (BKV), and simian virus 40 (SV40). Structural studies have elucidated agnoprotein's alpha-helical domains and roles in protein stability, while CRISPR-based genome-wide screens have identified critical host factors, such as methionine adenosyltransferase 2A (MAT2A) for BKV replication. These efforts have filled gaps in non-human polyomavirus research, with increased detection in avian species like psittacines and passerines, and fish, enhancing comparative virology. Long-standing concerns about SV40 contamination in polio vaccines administered from 1955 to 1963 have been addressed through epidemiological analyses, which found no significant increase in cancer risk among exposed cohorts, resolving the debate in favor of low oncogenic potential in humans. Looking ahead, vaccine development targets high-risk polyomaviruses, including JCV, with virus-like particle (VLP) formulations showing durable neutralizing antibody responses in preclinical models and potential for preventing progressive multifocal leukoencephalopathy in immunocompromised patients. Antiviral trials are progressing, such as phase I/II studies of cidofovir for BKV infections in transplant recipients, which found no significant antiviral effect despite good tolerability, and evaluations of brincidofovir, which inhibits polyomavirus replication in vivo.

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