rotavirus rotavirus rotavirus is a genus of double-stranded rna viruses in the family reoviridae. rotaviruses are the most common cause of diarrhoeal disease among infants and young children. nearly every child in the world is infected with a rotavirus at least once by the age of five. immunity develops with each infection, so subsequent infections are less severe. adults are rarely affected. there are nine species of the genus, referred to as a, b, c, d, f, g, h, i and j. rotavirus a, the most common species, causes more than 90% of rotavirus infections in humans. rotavirus computer–aided reconstruction of a rotavirus based on several electron micrographs virus classification (unranked): virus realm: riboviria kingdom: orthornavirae phylum: duplornaviricota class: resentoviricetes order: reovirales family: reoviridae subfamily: sedoreovirinae genus: rotavirus species rotavirus a rotavirus b rotavirus c rotavirus d rotavirus f rotavirus g rotavirus h rotavirus i rotavirus j the virus is transmitted by the faecal-oral route. it infects and damages the cells that line the small intestine and causes gastroenteritis (which is often called "stomach flu" despite having no relation to influenza). although rotavirus was discovered in 1973 by ruth bishop and her colleagues by electron micrograph images and accounts for approximately one third of hospitalisations for severe diarrhoea in infants and children, its importance has historically been underestimated within the public health community, particularly in developing countries. in addition to its impact on human health, rotavirus also infects other animals, and is a pathogen of livestock. rotaviral enteritis is usually an easily managed disease of childhood, but among children under 5 years of age rotavirus caused an estimated 151,714 deaths from diarrhoea in 2019. in the united states, before initiation of the rotavirus vaccination programme in the 2000s, rotavirus caused about 2.7 million cases of severe gastroenteritis in children, almost 60,000 hospitalisations, and around 37 deaths each year. following rotavirus vaccine introduction in the united states, hospitalisation rates have fallen significantly. public health campaigns to combat rotavirus focus on providing oral rehydration therapy for infected children and vaccination to prevent the disease. the incidence and severity of rotavirus infections has declined significantly in countries that have added rotavirus vaccine to their routine childhood immunisation policies. virology types of rotavirus there are nine species of rotavirus, referred to as a, b, c, d, f, g, h, i and j. humans are primarily infected by the species rotavirus a. a–i species cause disease in other animals, species h in pigs, d, f and g in birds, i in cats and j in bats. within the species 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. there are at least 36 g types and 51 p types but in infections of humans only a few combinations of g and p types predominate. they are g1p, g2p, g3p, g4p, g9p and g12p. structure 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. proteins 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 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. structural proteins 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-dependent 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 (lewis antigen system, abo blood group system and 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. this resistance is dependent on the rotavirus genotype. 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 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. nonstructural viral proteins 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. it is a viroporin that elevates cytosolic ca2+ in mammalian cells. 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)proteinuniprotmolecular weight kdalocationcopies per particlefunction 1 3302vp1p22678125at the vertices of the core12rna-dependent rna polymerase 2 2690vp2a2t3r5102forms inner shell of the core120rna binding 3 2591vp3a2t3s588at the vertices of the core12methyltransferase mrna capping enzyme 4 2362vp4a2t3t287surface spike180cell attachment, virulence 5 1611nsp1q99fx559nonstructural05'rna binding, interferon antagonist 6 1356vp6q6le8945inner capsid780structural and species-specific antigen 7 1104nsp3p0353637nonstructural0enhances viral mrna activity and shut-offs cellular protein synthesis 8 1059nsp2a2t3p035nonstructural0ntpase involved in rna packaging 9 1062vp71 vp72p0353338 and 34surface780structural and neutralisation antigen 10 751nsp4p0451220nonstructural0viroporin (enterotoxin) 11 667nsp5 nsp6a2t3q9 p1120322nonstructural0ssrna 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. replication a simplified drawing of the rotavirus replication cycle. the stages are:attachment of the virus to the host cells, which is mediated by vp4 and vp7penetration of the cell by the virus and uncoating of the viral capsidplus strand ssrna synthesis (this acts as the mrna) synthesis, which is mediated by vp1, vp3 and vp2formation of the viroplasm, viral rna packaging and minus strand rna synthesis and formation of the double-layered virus particlesvirus particle maturation and release of progeny virions the attachment of the virus to the host cell is initiated by vp4, which attaches to molecules, called glycans, on the surface of the cell. 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. transmission rotaviruses in the faeces of an infected child rotaviruses are transmitted by the faecal-oral route, via contact with contaminated hands, surfaces and objects, and possibly by the respiratory route. viral diarrhoea is highly contagious. the faeces of an infected person can contain more than 10 trillion infectious particles per gram; fewer than 100 of these are required to transmit infection to another person. rotaviruses are stable in the environment and have been found in estuary samples at levels up to 1–5 infectious particles per us gallon. the viruses survive between 9 and 19 days. sanitary measures adequate for eliminating bacteria and parasites seem to be ineffective in control of rotavirus, as the incidence of rotavirus infection in countries with high and low health standards is similar. signs and symptoms rotaviral enteritis is a mild to severe disease characterised by nausea, vomiting, watery diarrhoea and low-grade fever. once a child is infected by the virus, there is an incubation period of about two days before symptoms appear. the period of illness is acute. symptoms often start with vomiting followed by four to eight days of profuse diarrhoea. dehydration is more common in rotavirus infection than in most of those caused by bacterial pathogens, and is the most common cause of death related to rotavirus infection. rotavirus infections can occur throughout life: the first usually produces symptoms, but subsequent infections are typically mild or asymptomatic, as the immune system provides some protection. consequently, symptomatic infection rates are highest in children under two years of