Types of rotavirus
There are nine species of rotavirus, referred to as A, B, C, D, E, F, G, H and I. Humans are primarily infected by the species rotavirus A. A–E species cause disease in other animals, species E and H in pigs, D, F and G in birds and I in cats.
Within rotavirus A there are different strains, called serotypes. As with influenza virus, a dual classification system is used based on two proteins on the surface of the virus. The glycoprotein VP7 defines the G serotypes and the protease-sensitive protein VP4 defines P serotypes. Because the two genes that determine G-types and P-types can be passed on separately to progeny viruses, different combinations are found. A whole genome genotyping system has been established for rotavirus A, which has been used to determine the origin of atypical strains. The prevalence of the individual G-types and P-types varies between, and within, countries and years.
The genome of rotaviruses consists of 11 unique double helix molecules of RNA (dsRNA) which are 18,555 nucleotides in total. Each helix, or segment, is a gene, numbered 1 to 11 by decreasing size. Each gene codes for one protein, except genes 9, which codes for two. The RNA is surrounded by a three-layered icosahedral protein capsid. Viral particles are up to 76.5 nm in diameter and are not enveloped.
A simplified diagram of the location of rotavirus structural proteins
There are six viral proteins (VPs) that form the virus particle (virion). These structural proteins are called VP1, VP2, VP3, VP4, VP6 and VP7. In addition to the VPs, there are six nonstructural proteins (NSPs), that are only produced in cells infected by rotavirus. These are called NSP1, NSP2, NSP3, NSP4, NSP5 and NSP6.
At least six of the twelve proteins encoded by the rotavirus genome bind RNA. The role of these proteins play in rotavirus replication is not entirely understood; their functions are thought to be related to RNA synthesis and packaging in the virion, mRNA transport to the site of genome replication, and mRNA translation and regulation of gene expression.
Electron micrograph of gold nanoparticles attached to rotavirus. The small dark circular objects are gold nanoparticles coated with a monoclonal antibody
specific for rotavirus protein VP6.
VP1 is located in the core of the virus particle and is an RNA polymerase enzyme. In an infected cell this enzyme produces mRNA transcripts for the synthesis of viral proteins and produces copies of the rotavirus genome RNA segments for newly produced virus particles.
VP2 forms the core layer of the virion and binds the RNA genome.
VP3 is part of the inner core of the virion and is an enzyme called guanylyl transferase. This is a capping enzyme that catalyses the formation of the 5' cap in the post-transcriptional modification of mRNA. The cap stabilises viral mRNA by protecting it from nucleic acid degrading enzymes called nucleases.
VP4 is on the surface of the virion that protrudes as a spike. It binds to molecules on the surface of cells called receptors and drives the entry of the virus into the cell. VP4 has to be modified by the protease enzyme trypsin, which is found in the gut, into VP5* and VP8* before the virus is infectious. VP4 determines how virulent the virus is and it determines the P-type of the virus. In humans there is an association between the blood group secretor status and susceptibility to infection. Non-secretors seem resistant to infection by types P and P, indicating that blood group antigens are the receptors for these genotypes.
VP6 forms the bulk of the capsid. It is highly antigenic and can be used to identify rotavirus species. This protein is used in laboratory tests for rotavirus A infections.
VP7 is a glycoprotein that forms the outer surface of the virion. Apart from its structural functions, it determines the G-type of the strain and, along with VP4, is involved in immunity to infection.
NSP1, the product of gene 5, is a nonstructural RNA-binding protein. NSP1 also blocks the interferon response, the part of the innate immune system that protects cells from viral infection. NSP1 causes the proteosome to degrade key signaling components required to stimulate production of interferon in an infected cell and to respond to interferon secreted by adjacent cells. Targets for degradation include several IRF transcription factors required for interferon gene transcription.
NSP2 is an RNA-binding protein that accumulates in cytoplasmic inclusions (viroplasms) and is required for genome replication.
NSP3 is bound to viral mRNAs in infected cells and it is responsible for the shutdown of cellular protein synthesis. NSP3 inactivates two translation initiation factors essential for synthesis of proteins from host mRNA. First, NSP3 ejects poly(A)-binding protein (PABP) from the translation initiation factor eIF4F. PABP is required for efficient translation of transcripts with a 3' poly(A) tail, which is found on most host cell transcripts. Second, NSP3 inactivates eIF2 by stimulating its phosphorylation. Efficient translation of rotavirus mRNA, which lacks the 3' poly(A) tail, does not require either of these factors.
NSP4 is a viral enterotoxin that induces diarrhoea and was the first viral enterotoxin discovered.
NSP5 is encoded by genome segment 11 of rotavirus A. In virus-infected cells NSP5 accumulates in the viroplasm.
NSP6 is a nucleic acid binding protein and is encoded by gene 11 from an out-of-phase open reading frame.
Rotavirus genes and proteins
|RNA Segment (Gene)
||Size (base pairs)
||Molecular weight kDa
||Copies per particle
||At the vertices of the core
||RNA-dependent RNA polymerase
||Forms inner shell of the core
||At the vertices of the core
||methyltransferase mRNA capping enzyme
||Cell attachment, virulence
||5'RNA binding, interferon antagonist
||Structural and species-specific antigen
||Enhances viral mRNA activity and shut-offs cellular protein synthesis
||NTPase involved in RNA packaging
||38 and 34
||Structural and neutralisation antigen
||ssRNA and dsRNA binding modulator of NSP2, phosphoprotein
This table is based on the simian rotavirus strain SA11. RNA-protein coding assignments differ in some strains.
A simplified drawing of the rotavirus replication cycle. The stages are (1) attachment of the virus to the host cells, which is mediated by VP4 and VP7 (2) penetration of the cell by the virus and uncoating of the viral capsid (3) plus strand ssRNA synthesis ( this acts as the mRNA) synthesis, which is mediated by VP1, VP3 and VP2 (4) formation of the viroplasm, viral RNA packaging and minus strand RNA synthesis and formation of the double-layered virus particles (5) virus particle maturation and release of progeny virions.
The virus enters cells by receptor mediated endocytosis and form a vesicle known as an endosome. Proteins in the third layer (VP7 and the VP4 spike) disrupt the membrane of the endosome, creating a difference in the calcium concentration. This causes the breakdown of VP7 trimers into single protein subunits, leaving the VP2 and VP6 protein coats around the viral dsRNA, forming a double-layered particle (DLP).
The eleven dsRNA strands remain within the protection of the two protein shells and the viral RNA-dependent RNA polymerase creates mRNA transcripts of the double-stranded viral genome. By remaining in the core, the viral RNA evades innate host immune responses including RNA interference that are triggered by the presence of double-stranded RNA.
During the infection, rotaviruses produce mRNA for both protein biosynthesis and gene replication. Most of the rotavirus proteins accumulate in viroplasm, where the RNA is replicated and the DLPs are assembled. In the viroplasm the positive sense viral RNAs that are used as templates for the synthesis of viral genomic dsRNA are protected from siRNA-induced RNase degradation. Viroplasm is formed around the cell nucleus as early as two hours after virus infection, and consists of viral factories thought to be made by two viral nonstructural proteins: NSP5 and NSP2. Inhibition of NSP5 by RNA interference in vitro results in a sharp decrease in rotavirus replication. The DLPs migrate to the endoplasmic reticulum where they obtain their third, outer layer (formed by VP7 and VP4). The progeny viruses are released from the cell by lysis.