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Picornaviruses are a group of related Viral envelope which infect including fish, , and . They are that represent a large family of small, positive-sense, single-stranded RNA viruses with a 30 nm Icosahedron capsid. The viruses in this family can cause a range of diseases including the common cold, , meningitis, hepatitis, and paralysis. (2024). 9780128008386, Academic Press. ISBN 9780128008386
Picornaviruses constitute the Subfamily Picornaviridae, order Picornavirales, and realm Riboviria. There are 158 species in this family, assigned to 68 genera. Notable examples are genera Enterovirus (including Rhinovirus and Poliovirus), Aphthovirus, Cardiovirus, and Hepatovirus.
Many picornaviruses have a deep cleft formed by around each of the 12 vertices of icosahedrons. The outer surface of the capsid is composed of regions of VP1, VP2, and VP3. Around each of the vertices is a canyon lined with the C termini of VP1 and VP3. The interior surface of the capsid is composed of VP4 and the N termini of VP1. J. Esposito and Frederick A. Murphy demonstrates cleft structure referred to as canyons, using X-ray crystallography and cryoelectron microscopy.
Depending on the type and degree of dehydration, the viral particle is around 30–32 nm in diameter. The viral genome is around 2500 nm in length, so it is tightly packaged within the capsid along with substances such as sodium ions to balance the negative charges on the RNA caused by the phosphate groups.
The genome is not 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. An untranslated region (UTR) is found 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. The 5' UTR is thought to be 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 nonstructural proteins at the 3' end in a single polyprotein.
The polyprotein is organised as: L-1ABCD-2ABC-3ABCD with each letter representing a protein, but variations to this layout exist.
The 1A, 1B, 1C, and 1D proteins are the capsid proteins VP4, VP2, VP3, and VP1, respectively. Virus-coded proteases perform the cleavages, some of which are intramolecular. The polyprotein is first cut to yield P1, P2, and P3. P1 becomes myristylated at the N terminus before being cleaved to VP0, VP3, and VP1, the proteins that will form procapsids; VP0 will later be cleaved to produce VP2 and VP4. Other cleavage products include 3B (VPg), 2C (an ATPase), and 3D (the RNA polymerase).
Once inside the cell, the RNA uncoats and the (+) strand RNA genome is replicated through a double-stranded RNA intermediate that is formed using viral 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 internal ribosome entry site. The viral life cycle is very rapid, with the whole process of replication being completed on average within 8 hours. As little as 30 minutes after initial infection, though, cell protein synthesis declines to almost zero output – essentially the macromolecular synthesis of cell proteins is shut off. Over the next 1–2 hours, a loss of margination of chromatin and occurs 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. 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 observation of 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 cell nucleus (enucleated) and those treated with actinomycin D (this antibiotic would inhibit viral replication if this occurred in the nucleus.)
Translation takes place by -1 ribosomal frameshifting, viral initiation, and ribosomal skipping. The virus exits in host cell by lysis, and viroporins. Vertebrates serve as the natural hosts. Transmission routes are fecal-oral, contact, ingestion, and air-borne particles.
In this group, primer-dependent RNA synthesis uses a small 22– to 25-amino acid-long viral protein linked to the VPg to initiate polymerase activity, where the primer is covalently bound to the 5' end of the RNA template. The uridylylation occurs at a tyrosine residue at the third position of the VPg. A 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. 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. 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 and coxsackie virus B3 suggest that there may be two sites on the viral polymerase for the small VPgs of the picornaviruses. NMR solution structures of poliovirus VPg and VPgpU show that uridylylation stabilizes the structure of the VPg, which is otherwise quite flexible in solution. The second site may be used for uridylylation,v after which the VPgpU can initiate RNA synthesis. The VPg primers of caliciviruses, whose structures are only beginning to be revealed, 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 positive- or negative-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. Precursor proteins also have an effect on VPg-CRE specificity and stability. 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, but no consensus sequence exists for the supporting stem, which suggests that only the structural stability of the CRE is important.
VPg may also play an important role in specific recognition of viral genome by movement proteins (MP), which are nonstructural proteins encoded by many, if not all, plant viruses to enable their movement from one infected cell to neighboring cells. 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.
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