Polyomaviridae

Polyomaviridae
Micrograph showing a polyomavirus infected cell—large (blue) cell below-center-left. Urine cytology specimen.
Virus classification
Group: Group I (dsDNA)
Family: Polyomaviridae
Genera

Polyomaviridae is a family of viruses whose natural hosts are primarily mammals and birds. As of the most recent (2015) taxonomy release by the International Committee on Taxonomy of Viruses, there were 73 recognized species in this family contained within four genera, as well as three species that could not be assigned to a genus.[1] Of these, 13 species are known to infect humans.[2][3] Most of these viruses, such as BK virus and JC virus, are very common and typically asymptomatic in most human populations studied.[4][5] However, some polyomaviruses are associated with human disease, particularly in immunocompromised individuals; BK virus is associated with nephropathy in renal transplant and non-renal solid organ transplant patients,[6][7] JC virus with progressive multifocal leukoencephalopathy,[8] and Merkel cell virus with Merkel cell cancer.[9]

Some members of the family are oncoviruses, meaning they can cause tumors; they often persist as latent infections in a host without causing disease, but may produce tumors in a host of a different species, or in individuals with ineffective immune systems. The family was first discovered due to its oncogenic properties; some members of the family, most prominently murine polyomavirus, have been extensively studied in the laboratory to understand the mechanism by which they induce carcinogenesis. The name polyoma refers to the viruses' ability to produce multiple (poly-) tumors (-oma).

Structure and genome

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 further away appear red. Rendered from PDB: 1SIE​.

Polyomaviruses are unenveloped double-stranded DNA viruses with circular genomes of around 5000 base pairs. The genome is packaged in a viral capsid of about 40-50 nanometers in diameter, which is icosahedral in shape (T=7 symmetry).[10] The capsid is composed of 72 pentamers of a protein called VP1, which is capable of self-assembly into a closed icosahedron;[11] each molecule of VP1 is associated with one molecule of one of the other two capsid proteins, VP2 or VP3.[12]

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.[13]

The genome of a typical polyomavirus codes for between 5 and 9 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.[10][12]

Genus Structure Symmetry Capsid Genomic arrangement Genomic segmentation
PolyomavirusIcosahedralT=7Non-EnvelopedCircularMonopartite

Replication and life cycle

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​.[14]

Prior to genome replication, the processes of viral attachment, entry and uncoating occur. 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.[14]

Polyomavirus virions are subsequently endocytosed and transported first to the endoplasmic reticulum where a conformational change occurs revealing Vp2. Then by an unknown mechanism the virus is exported to the nucleus.

Polyomaviruses replicate in the nucleus of the host. They are able to utilise the host’s machinery because the genomic structure is homologous to that of the mammalian host. Moreover, the promoter sequence of Polyomavirus' promoter sequence is a strong attractant for the host's RNAP. Viral replication occurs in two distinct phases; early and late gene expression, separated by genome replication.

Early gene expression is responsible for the synthesis of non-structural proteins. Since Polyomaviruses rely on the host to control both the gene expression, the role of the non-structural proteins is to regulate the cellular mechanisms. Close to the N terminal end of polyomavirus genome are enhancer elements which induce activation and transcription of a molecule known as the T-antigen (see SV40 large T-antigen). Early mRNA’s, encoding T-antigen are produced by host RNA polymerase II. T-antigen autoregulates early mRNA’s, subsequently leading to elevated levels of T-antigen. At high concentrations of T-antigen, early gene expression is repressed, triggering the late phase of viral infection to begin.

Genome replication acts to separate the early and late phase gene expression. The duplicated viral genome is synthesised and processed as if it were cellular DNA, exploiting the host’s machinery. As the daughter viral DNA are synthesised they associate with cellular nucleosomes to form structures that are often referred to as "minichromosomes". In this manner the DNA is packaged more efficiently.

Late gene expression synthesises the structural proteins, responsible for the viral particle composition. This occurs during and after genome replication. As with the early gene expression products, late gene expression generates an array of proteins as a result of alternative splicing.

Within each viral protein are 'nuclear localization signals' which cause the viral proteins to amass in the nucleus. Assembly of new virus particles consequently occurs within the nucleus of the host cell.[15]

Release of newly synthesized polyomavirus particles exit the infected cell by one of two mechanisms. Firstly and less commonly, they are transported in cytoplasmic vacuoles to the plasma membrane, where budding occurs. More frequently, they are released when the cell lyses due to the cytotoxicity of virus particles present in the infected cell.

Genus Host details Tissue tropism Entry details Release details Replication site Assembly site Transmission
PolyomavirusMammals; birdsRespiratory system; kidneys, brainCell receptor endocytosisLysisNucleusNucleusOral-fecal

Viral proteins

The polyoma large and small T-antigens

The large T-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.[16] This is achieved by a two prong attack of inhibiting tumor suppressing genes p53 and members of the retinoblastoma (pRB) family,[17] and stimulating cell growth pathways by binding cellular DNA, ATPase-helicase, DNA polymerase α association, and binding of transcription preinitiation complex factors.[18] This abnormal stimulation of the cell cycle is a powerful force for oncogenic transformation.

The small T-antigen protein is also able to activate several cellular pathways that stimulate cell proliferation. Polyomavirus small T antigens commonly target protein phosphatase 2A (PP2A),[19] a key multisubunit regulator of multiple pathways including Akt, the mitogen-activated protein kinase (MAPK) pathway, and the stress-activated protein kinase (SAPK) pathway.[20][21] 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.[22] Unlike for SV40, the MCV small T antigen directly transforms rodent cells in vitro.[23]

The polyoma middle T-antigen

The polyoma middle T-antigen is used in animal breast cancer model systems like the PYMT system where it 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.

Agnoprotein

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.[24][25]

Taxonomy

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.[1] (The name Papovaviridae derived from three abbreviations: Pa for Papillomavirus, Po for Polyomavirus, and Va for "vacuolating.")[26] The polyomaviruses were divided into three major clades (that is, genetically-related groups): the SV40 clade, the avian clade, and the murine polyomavirus clade.[27] A subsequent proposed reclassification by the International Committee on Taxonomy of Viruses (ICTV) recommended dividing the family of Polyomaviridae into three genera:[28]

The current ICTV classification system recognises four genera and 76 species, of which three could not be assigned a genus. This system retains the distinction between avian and mammalian viruses, grouping the avian subset into the genus Gammapolyomavirus.[1][2]

Human polyomaviruses

Most polyomaviruses do not infect humans. Of the polyomaviruses cataloged as of 2016, a total of 13 were known with human hosts.[2] Many human polyomaviruses are very common and are asymptomatic.[4][5] 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).

List of human polyomaviruses

The following 13 polyomaviruses with human hosts had been identified and had their genomes sequenced as of 2016:[2]

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[12] [29][30][31]
Human polyomavirus 8 Alpha Trichodysplasia spinulosa polyomavirus TSPyV NC_014361 2010 Trichodysplasia spinulosa[12] [32][33]
Human polyomavirus 9 Alpha Human polyomavirus 9 HPyV9 NC_015150 2011 None known [34]
Human polyomavirus 12 Alpha Human polyomavirus 12 HPyV12 NC_020890 2013 None known [35]
Human polyomavirus 13 Alpha New Jersey polyomavirus NJPyV NC_024118 2014 None known [36]
Human polyomavirus 1 Beta BK polyomavirus BKPyV NC_001538 1971 Polyomavirus-associated nephropathy; haemorrhagic cystitis[12] [37]
Human polyomavirus 2 Beta JC polyomavirus JCPyV NC_001699 1971 Progressive multifocal leukoencephalopathy[12] [38]
Human polyomavirus 3 Beta KI polyomavirus KIPyV NC_009238 2007 None known [39]
Human polyomavirus 4 Beta WU polyomavirus WUPyV NC_009539 2007 None known [40]
Human polyomavirus 6 Delta Human polyomavirus 6 HPyV6 NC_014406 2010 None known [41]
Human polyomavirus 7 Delta Human polyomavirus 7 HPyV7 NC_014407 2010 HPyV7-related epithelial hyperplasia[42][43] [41]
Human polyomavirus 10 Delta MW polyomavirus MWPyV NC_018102 2012 None known [44][45][46]
Human polyomavirus 11 Delta STL polyomavirus SLTPyV NC_020106 2013 None known [47]

The proposed Deltapolyomavirus genus contains only the four human viruses shown, with human polyomavirus 6 as the type species. The Alpha and Beta groups contain viruses that infect a variety of mammals. The Gamma group contains the avian viruses.[2] Clinically significant disease associations are shown only where causality is expected.[12][48]

Clinical relevance

All the polyomaviruses are highly common childhood and young adult infections.[49] 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,[6][7] JC virus with progressive multifocal leukoencephalopathy,[8] and Merkel cell virus (MCV) with Merkel cell cancer.[9]

SV40

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.[50][51] Although it has been reported as present in some human cancers, including brain tumors, bone tumors, mesotheliomas, and non-Hodgkin's lymphomas,[52] accurate detection is often confounded by high levels of cross-reactivity for SV40 with widespread human polyomaviruses.[51] Most virologists dismiss SV40 as a cause for human cancers.[50][53][54]

Diagnosis

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.[55] Competition assays are frequently needed to distinguish among highly similar polyomaviruses.[56]

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.[57]

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.[55] 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.[58] Also as the urine of an infected individual will contain virions and/or viral DNA, quanitation of the viral load can be done through PCR.[59] 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.

Tissue staining using a monoclonal antibody against MCV T antigen shows utility in differentiating Merkel cell carcinoma from other small, round cell tumors.[60] 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.[61][62][63][64]

History

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.[65] The causative agent was identified as a virus by Sarah Stewart and Bernice Eddy, after whom it was once called "SE polyoma".[66][67][68] 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.[69]

Dozens of polyomaviruses have been identified and sequenced as of 2016, infecting mainly birds and mammals. Two polyomaviruses are known to infect fish, the black sea bass[70] and gilthead seabream.[71] A total of thirteen polyomaviruses are known to infect humans.[2]

References

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