Picornavirus

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Picornavirus
Virus classification
Group: Group IV ((+)ssRNA)
Order: Picornavirales
Family: Picornaviridae
Genera

A picornavirus is a virus belonging to the family Picornaviridae. Picornaviruses are non-enveloped, positive-stranded RNA viruses with an icosahedral capsid. The genome RNA is unusual because it has a protein on the 5' end that is used as a primer for transcription by RNA polymerase. The name is derived from pico, meaning small, and RNA, referring to the ribonucleic acid genome, so "pico-rna-virus" literally means small RNA virus.

Picornaviruses are separated into a number of genera and include many important pathogens of humans and animals.[1] The diseases they cause are varied, ranging from acute "common-cold"-like illnesses, to polio, to chronic livestock infections. Additional species not belonging to any of the recognised genera continue to be described.[2]

Taxonomy[edit]

Picornaviruses are separated into a number of genera. Contained within the picornavirus family are many organisms of importance as vertebrate and human pathogens, shown in the table below.

Enteroviruses infect the enteric tract, which is reflected in their name. On the other hand, rhinoviruses infect primarily the nose and the throat. Enteroviruses replicate at 37°C, whereas rhinoviruses grow better at 33°C, as this is the lower temperature of the nose. Enteroviruses are stable under acid conditions and thus they are able to survive exposure to gastric acid. In contrast, rhinoviruses are acid-labile (inactivated or destroyed by low pH conditions) and that is the reason why rhinovirus infections are restricted to the nose and throat.

Picornavirus Genera, Species and Serotypes
Genus Species (* signifies type species) Serotypes
Aphthovirus Bovine rhinitis A virus 2 types: bovine rhinitis A virus (BRAV) 1–2 (formerly bovine rhinovirus 1 & 3)
Bovine rhinitis B virus 1 type: bovine rhinitis B virus (BRBV) 1 (formerly bovine rhinovirus 2)
Equine rhinitis A virus 1 type: equine rhinitis A virus (ERAV) 1 (formerly equine rhinovirus 1)
Foot-and-mouth disease virus[3] * 7 types: O, A, C, Southern African Territories (SAT) 1, SAT 2, SAT 3 and Asia 1
Aquamavirus Aquamavirus A 1 type: seal aquamavirus A1 (SeAV-A1)
Avihepatovirus Duck hepatitis A virus 3 types: duck hepatitis A virus (DHAV) 1–3
Cardiovirus Encephalomyocarditis virus * 2 types: encephalomyocarditis virus (EMCV) 1 & EMCV-2. Note: Columbia SK virus, Maus Elberfeld virus and Mengovirus are strains of EMCV-1.
Theilovirus 12 types: Theiler's murine encephalomyelitis virus (TMEV), Vilyuisk human encephalomyelitis virus (VHEV), Thera virus (TRV), Saffold virus (SAFV) 1–9
Cosavirus Cosavirus A 24 types: cosavirus A1 (CoSV-A1) to CoSV-A24
Dicipivirus Cadicivirus A 1 type: canine picodicistrovirus 1 (CaPdV-1)
Enterovirus Enterovirus A (formerly Human enterovirus A) 23 types: coxsackievirus A2 (CV-A2), CV-A3, CV-A4, CV-A5, CV-A6, CV-A7, CV-A8, CV-A10, CV-A12, CV-A14, CV-A16, enterovirus (EV) A71, EV-A76, EV-A89, EV-A90, EV-A91, EV-A92, EV-114, EV-A119, SV19, SV43, SV46 & BA13; see also coxsackie A virus
Enterovirus B (formerly Human enterovirus B) 60 types: coxsackievirus B1 (CV-B1), CV-B2, CV-B3, CV-B4, CV-B5 (incl. swine vesicular disease virus [SVDV]), CV-B6, CV-A9, echovirus 1 (E-1; incl. E-8), E-2, E-3, E-4, E-5, E-6, E-7, E-9 (incl. CV-A23), E-11, E-12, E-13, E-14, E-15, E-16, E-17, E-18, E-19, E-20, E-21, E-24, E-25, E-26, E-27, E-29, E-30, E-31, E-32, E-33, enterovirus B69 (EV-B69), EV-B73, EV-B74, EV-B75, EV-B77, EV-B78, EV-B79, EV-B80, EV-B81, EV-B82, EV-B83, EV-B84, EV-B85, EV-B86, EV-B87, EV-B88, EV-B93, EV-B97, EV-B98, EV-B100, EV-B101, EV-B106, EV-B107, EV-B110 & SA5; see also coxsackie B virus and echovirus
Enterovirus C * (formerly Human enterovirus C) 23 types: poliovirus (PV) 1, PV-2, PV-3, coxsackievirus A1 (CV-A1), CV-A11, CV-A13, CV-A17, CV-A19, CV-A20, CV-A21, CV-A22, CV-A24, EV-C95, EV-C96, EV-C99, EV-C102, EV-C104, EV-C105, EV-C109, EV-C113, EV-C116, EV-C117 & EV-118
Enterovirus D (formerly Human enterovirus D) 5 types: enterovirus D68 (EV-D68), EV-D70, EV-D94, EV-D111 & EV-D120
Enterovirus E (formerly Bovine enterovirus group A) 4 types (proposed): enterovirus E1 (EV-E1), EV-E2, EV-E3 & EV-E4
Enterovirus F (formerly Bovine enterovirus group B) 6 types (proposed): enterovirus F1 (EV-F1), EV-F2, EV-F3, EV-F4, EV-F5 & EV-E6
Enterovirus G (formerly Porcine enterovirus B) 6 types: enterovirus (EV) G1 to G6 (formerly porcine enterovirus 9–10, 14–16 and ovine enterovirus 1)
Enterovirus H (formerly Simian enterovirus A) 1 type: enterovirus H1 (EV-H1)
Enterovirus J 6 types: simian virus 6 (SV6), enterovirus J103 (EV-J103), EV-J108, EV-J112, EV-J115 and EV-J121
Rhinovirus A (formerly Human rhinovirus A) 77 types: human rhinovirus (HRV) A1, A2, A7, A8, A9, A10, A11, A12, A13, A15, A16, A18, A19, A20, A21, A22, A23, A24, A25, A28, A29, A30, A31, A32, A33, A34, A36, A38, A39, A40, A41, A43, A44, A45, A46, A47, A49, A50, A51, A53, A54, A55, A56, A57, A58, A59, A60, A61, A62, A63, A64, A65, A66, A67, A68, A71, A73, A74, A75, A76, A77, A78, A80, A81, A82, A85, A88, A89, A90, A94, A95, A96, A98, A100, A101, A102 and A103
Rhinovirus B (formerly Human rhinovirus B) 25 types: human rhinovirus (HRV) B3, B4, B5, B6, B14, B17, B26, B27, B35, B37, B42, B48, B52, B69, B70, B72, B79, B83, B84, B86, B91, B92, B93, B97 and B99
Rhinovirus C (formerly Human rhinovirus C) 51 types: human rhinovirus (HRV) C1–C51
Erbovirus Equine rhinitis B virus * 3 types: equine rhinitis B virus (ERBV) 1–3 (formerly equine rhinovirus 2, 3 and acid-stable equine picornavirus)
Hepatovirus Hepatitis A virus * 1 type: hepatitis A virus (HAV) 1
Kobuvirus Aichivirus A * (formerly Aichi virus) 3 types: Aichi virus (AiV) 1, canine kobuvirus 1 (CaKV-1) & murine kobuvirus 1 (MuKV-1)
Aichivirus B (formerly Bovine kobuvirus) 2 types: bovine kobuvirus (BKV) 1 & ovine kobuvirus 1 (OKV-1)
Aichivirus C 1 type: porcine kobuvirus 1 (PKV-1)
Megrivirus Melegrivirus A * 1 type: turkey hepatitis virus (THV) 1
Parechovirus Human parechovirus * 14 types: human parechovirus (HPeV) 1-14
Ljungan virus 4 types: Ljungan virus (LV) 1–4
Piscevirus Fathead minnow picornavirus 1 type: Fathead minnow picornavirus
Salivirus Salivirus A 1 type: salivirus A1
Sapelovirus Porcine sapelovirus * (formerly Porcine enterovirus A) 1 type: porcine sapelovirus (PSV) 1 (formerly PEV-8)
Simian sapelovirus 3 types: simian sapleovirus (SSV) 1–3
Avian sapelovirus 1 type: avian sapelovirus (ASV) 1
Senecavirus Seneca Valley virus * 1 type: Seneca Valley virus (SVV) 1
Teschovirus Porcine teschovirus * 13 types: porcine teschovirus (PTV) 1 to 13
Tremovirus Avian encephalomyelitis virus 1 type: avian encephalomyelitis virus (AEV) 1

Plant picornaviruses[edit]

The plant picornaviruses have a number of properties that are distinct from the animal viruses. They have been classified into the family Secoviridae containing the subfamily Comovirinae (genera Comovirus, Fabavirus and Nepovirus), and genera Sequivirus, Waikavirus, Cheravirus, Sadwavirus and Torradovirus (type species Tomato torrado virus)).

Insect picornaviruses[edit]

A number of picorna like viruses have been described infecting insects. These include Perina nuda picorna-like virus of the tussock moth, infectious flacherie virus of the silkworm and Sacbrood virus of the honeybee,[4] Plautia stali intestine virus[5] kelp fly virus,[6] Ectropis obliqua picorna-like virus,[7] deformed wing virus,[8] acute bee paralysis virus, Drosophila C virus, Rhopalosiphum padi virus, and Himetobi P virus.[9] Several have been placed in a separate family—the Dicistroviridae. Others have been placed into a new family Iflaviridae. This family includes Infectious flacherie virus and SeIV-1 virus.[10] Another virus is Nora virus from Drosophila melanogaster. This latter virus awaits further classification.

Virology[edit]

Picornaviruses are classed under Baltimore's viral classification system as group IV viruses as they contain a single stranded, positive sense RNA genome of between 7.2 and 9.0 kb (kilobases) in length. Like most positive sense RNA genomes, the genetic material alone is infectious; although substantially less virulent than if contained within the viral particle, the RNA can have increased infectivity when transfected into cells.

Structure[edit]

The capsid is an arrangement of 60 protomers in a tightly packed icosahedral structure. Each protomer consists of 4 polypeptides known as VP (viral protein)1, 2, 3 and 4. VP2 and VP4 polypeptides originate from one protomer known as VP0 that is cleaved to give the different capsid components. The icosahedral is said to have a triangulation number of 3, this means that in the icosahedral structure each of the 60 triangles that make up the capsid are split into 3 little triangles with a subunit on the corner. Depending on the type and degree of dehydration the viral particle is around 27–30 nm in diameter. The viral genome is around 2500 nm in length so we can therefore conclude that it must be tightly packaged within the capsid along with substances such as sodium ions in order to cancel out the negative charges on the RNA caused by the phosphate groups.

Genome[edit]

The genome itself is non-segmented and positive-sense (the same sense as mammalian mRNA, being read 5' to 3'). Unlike mammalian mRNA picornaviruses do not have a 5' cap but a virally encoded protein known as VPg. However, like mammalian mRNA, the genome does have a poly(A) tail at the 3' end. There is an un-translated region (UTR) at both ends of the picornavirus genome. The 5' UTR is usually longer, being around 500–1200 nucleotides (nt) in length, compared to that of the 3' UTR, which is around 30–650 nt. It is thought that the 5' UTR is important in translation and the 3' in negative strand synthesis; however the 5' end may also have a role to play in virulence of the virus. The rest of the genome encodes structural proteins at the 5' end and non-structural proteins at the 3' end in a single polyprotein.

The polyprotein is organised as follows: L-1ABCD-2ABC-3ABCD with each letter representing a protein, however, there are variations to this layout.

The 1A, 1B, 1C, and 1D proteins are the capsid proteins VP4, VP2, VP3, and VP1, respectively. VP0 is cleaved into VP2 and VP4 during virion maturation, after the capsid has been formed. The L, 2A, and 3C proteins are proteinases that internally cleave the polyprotein, but these roles vary between genera of picornaviruses. The 2B, 2C, and 3A proteins interfere with host cell function. The 3B protein is the VPg protein. The 3D protein is the RNA polymerase.[11]

Replication[edit]

The viral particle binds to cell surface receptors. This causes a conformational change in the viral capsid proteins, and myristic acid are released. These acids form a pore in the cell membrane through which RNA is injected [2]. Once inside the cell, the RNA un-coats and the (+) strand RNA genome is replicated through a double-stranded RNA intermediate that is formed using viral RDRP (RNA-Dependent RNA polymerase). Translation by host cell ribosomes is not initiated by a 5' G cap as usual, but rather is initiated by an IRES (Internal Ribosome Entry Site). The viral lifecycle is very rapid with the whole process of replication being completed on average within 8 hours. However as little as 30 minutes after initial infection, cell protein synthesis declines to almost zero output – essentially the macromolecular synthesis of cell proteins is “shut off”. Over the next 1–2 hours there is a loss of margination of chromatin and homogeneity in the nucleus, before the viral proteins start to be synthesized and a vacuole appears in the cytoplasm close to the nucleus that gradually starts to spread as the time after infection reaches around 3 hours. After this time the cell plasma membrane becomes permeable, at 4–6 hours the virus particles assemble, and can sometimes be seen in the cytoplasm. At around 8 hours the cell is effectively dead and lyses to release the viral particles.

Experimental data from single step growth-curve-like experiments have allowed scientists to look at the replication of the picornaviruses in great detail. The whole of replication occurs within the host cell cytoplasm and infection can even happen in cells that do not contain a nucleus (known as enucleated cells) and those treated with actinomycin D (this antibiotic would inhibit viral replication if this occurred in the nucleus.)

VPg[edit]

A VPg primer mechanism is utilized by the picornavirus (entero- aphtho- and others), additional virus groups (poty-, como-, calici- and others) and picornavirus-like (coronavirus, notavirus, etc.) supergroup of RNA viruses. The mechanism has been best studied for the enteroviruses (which include many human pathogens, such as poliovirus and coxsackie viruses) as well as for the aphthovirus, an animal pathogen causing foot and mouth disease (FMDV).

In this group, primer-dependent RNA synthesis utilizes a small 22–25 amino acid long viral protein linked to the genome (VPg)[12] to initiate polymerase activity, where the primer is covalently bound to the 5’ end of the RNA template.[13] The uridylylation occurs at a tyrosine residue at the third position of the VPg. A cis-acting replication element (CRE), which is a RNA stem loop structure, serves as a template for the uridylylation of VPg, resulting in the synthesis of VPgpUpUOH. Mutations within the CRE-RNA structure prevent VPg uridylylation, and mutations within the VPg sequence can severely diminish RdRp catalytic activity.[14] While the tyrosine hydroxyl of VPg can prime negative-strand RNA synthesis in a CRE- and VPgpUpUOH-independent manner, CRE-dependent VPgpUpUOH synthesis is absolutely required for positive-strand RNA synthesis. CRE-dependent VPg uridylylation lowers the Km¬ of UTP required for viral RNA replication and CRE-dependent VPgpUpUOH synthesis, and is required for efficient negative-strand RNA synthesis, especially when UTP concentrations are limiting.[15] The VPgpUpUOH primer is transferred to the 3’ end of the RNA template for elongation, which can continue by addition of nucleotide bases by RdRp. Partial crystal structures for VPgs of foot and mouth disease virus[16] and coxsackie virus B3[17] suggest that there may be two sites on the viral polymerase for the small VPgs of the picornaviruses. NMR solution structures of poliovirus VPg[18] and VPgpU[19] show that uridylylation stabilizes the structure of the VPg, which is otherwise quite flexible in solution. The second site may be used for uridylylation,[20] after which the VPgpU can initiate RNA synthesis. It should be noted that the VPg primers of caliciviruses, whose structures are only beginning to be revealed,[21] are much larger than those of the picornaviruses. Mechanisms for uridylylation and priming may be quite different in all of these groups.

VPg uridylylation may include the use of precursor proteins, allowing for the determination of a possible mechanism for the location of the diuridylylated, VPg-containing precursor at the 3’ end of plus- or minus-strand RNA for production of full-length RNA. Determinants of VPg uridylylation efficiency suggest formation and/or collapse or release of the uridylylated product as the rate-limiting step in vitro depending upon the VPg donor employed.[22] Precursor proteins also have an effect on VPg-CRE specificity and stability.[23] The upper RNA stem loop, to which VPg binds, has a significant impact on both retention, and recruitment, of VPg and Pol. The stem loop of CRE will partially unwind, allowing the precursor components to bind and recruit VPg and Pol4. The CRE loop has a defined consensus sequence to which the initiation components bind, however; there is no consensus sequence for the supporting stem, which suggests that only the structural stability of the CRE is important.[24]

Assembly and organization of the picornavirus VPg ribonucleoprotein complex.

  • Step 1: Two 3CD (VPg complex) molecules bind to CRE with the 3C domains (VPg domain) contacting the upper stem and the 3D domains (VPg domain) contacting the lower stem.
  • Step 2: The 3C dimer opens the RNA stem by forming a more stable interaction with single strands forming the stem.
  • Step 3: 3Dpol is recruited to and retained in this complex by a physical interaction between the back of the thumb subdomain of 3Dpol and a surface of one or both 3C subdomains of 3CD.

VPg may also play an important role in specific recognition of viral genome by movement protein (MP). Movement proteins are non-structural proteins encoded by many, if not all, plant viruses to enable their movement from one infected cell to neighboring cells.[25] MP and VPg interact to provide specificity for the transport of viral RNA from cell to cell. To fulfill energy requirements, MP also interacts with P10, which is a cellular ATPase.

History[edit]

In 1897, foot-and-mouth disease virus (FMDV), the first animal virus, was discovered. FMDV is the prototypic member of the Aphthovirus genus in the Picornaviridae family.[3] The plaque assay was developed using poliovirus. Both RNA dependent RNA polymerase and polyprotein synthesis were discovered by studying poliovirus infected cells.

See also[edit]

References[edit]

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