Orthoflavivirus
Orthoflavivirus is a genus of positive-strand RNA viruses in the family Flaviviridae. The genus includes the West Nile virus, dengue virus, tick-borne encephalitis virus, yellow fever virus, Zika virus and several other viruses which may cause encephalitis, as well as insect-specific flaviviruses such as cell fusing agent virus, Palm Creek virus, and Parramatta River virus. While dual-host flaviviruses can infect vertebrates as well as arthropods, insect-specific flaviviruses are restricted to their competent arthropods. The means by which flaviviruses establish persistent infection in their competent vectors and cause disease in humans depends upon several virus-host interactions, including the intricate interplay between flavivirus-encoded immune antagonists and the host antiviral innate immune effector molecules.
Orthoflaviviruses are named for the yellow fever virus; the word flavus means 'yellow' in Latin, and yellow fever in turn is named from its propensity to cause yellow jaundice in victims.
Orthoflaviviruses share several common aspects: common size, symmetry, nucleic acid, and appearance under the electron microscope.
Most of these viruses are primarily transmitted by the bite from an infected arthropod, and hence are classified as arboviruses. Human infections with most of these arboviruses are incidental, as humans are unable to replicate the virus to high enough titers to reinfect the arthropods needed to continue the virus life-cycle – humans are then a dead end host. The exceptions to this are the yellow fever virus, Dengue virus and Zika virus. These three viruses still require mosquito vectors but are well-enough adapted to humans as to not necessarily depend upon animal hosts.
Other virus transmission routes for arboviruses include handling infected animal carcasses, blood transfusion, sex, childbirth and consumption of unpasteurised milk products. Transmission from nonhuman vertebrates to humans without an intermediate vector arthropod however mostly occurs with low probability. For example, early tests with yellow fever showed that the disease is not contagious.
The known non-arboviruses of the flavivirus family reproduce in either arthropods or vertebrates, but not both, with one odd member of the genus affecting a nematode.
History and name
Yellow fever is the first human viral disease extensively investigated and the nature of the infection established. In 1900, the U.S. military programme, the Yellow Fever Commission, announced that the disease was transmitted by mosquitoes. In 1927, a British physician Adrian Stokes identified the virus in Ghana.Other viruses like West Nile virus, Japanese encephalitis virus, tick-borne encephalitis virus, Zika virus and dengue virus were subsequently discovered in the early 20th century. When the authority on viral classification, the International Committee on Nomenclature of Viruses, published it first report in 1971, all the viruses were grouped under the genus Arbovirus group B. In 1974, the ICNV created a more technical name following biological nomenclature, Flavivirus; derived from Latin flavi, as Yellow fever virus was accepted as the type species. ICNV also changed its name to the International Committee on Taxonomy of Viruses. The family name Togaviridae was also created for the virus group, which was changed to Flaviviridae in 1984.
It was the customary to call members of Flaviviridae and its genus Flavivirus by common names like flavivirus, flaviviral, and flaviviruses. However, the confusion arose when other viruses of the family but different genera were described such as Hepacivirus, Pegivirus, and Pestivirus. To resolve the issue, ICTV decided in 2022 to change the genus name to Orthoflavivirus, which was adopted in 2023. By the new name, the genus Orthoflavivirus should be known by vernacular names like orthoflavivirus, orthoflaviviral or orthoflaviviruses. According to ICTV resolution:
To preclude this potential confusion, a taxonomic proposal was submitted to the ICTV in 2022. It proposed that the genus Flavivirus be renamed Orthoflavivirus, which roughly translates to "true flaviviruses" or "flaviviruses sensu stricto". This proposal was approved by the ICTV Executive Committee in late 2022 and ratified by the ICTV in April 2023. Consequently, the terms "flaviviral", "flavivirus", and "flaviviruses" should be used to refer to the collective members of the family Flaviviridae, whereas the terms "orthoflaviviral", "orthoflavivirus", and "orthoflaviviruses" should be used for viruses of the genus Orthoflavivirus.
Structure
Orthoflaviviruses are enveloped and spherical and have icosahedral geometries with a pseudo T=3 symmetry. The virus particle diameter is around 50 nm.Genome
Orthoflaviviruses have positive-sense, single-stranded RNA genomes which are non-segmented and around 10–11 kbp in length. In general, the genome encodes three structural proteins and seven non-structural proteins. The genomic RNA is modified at the 5′ end of positive-strand genomic RNA with a cap-1 structure.Life cycle
Orthoflaviviruses replicate in the cytoplasm of the host cells. The genome mimics the cellular mRNA molecule in all aspects except for the absence of the poly-adenylated tail. This feature allows the virus to exploit cellular apparatuses to synthesize both structural and non-structural proteins, during replication. The cellular ribosome is crucial to the replication of the flavivirus, as it translates the RNA, in a similar fashion to cellular mRNA, resulting in the synthesis of a single polyprotein.Cellular RNA cap structures are formed via the action of an RNA triphosphatase, with guanylyltransferase, N7-methyltransferase and 2′-O methyltransferase. The virus encodes these activities in its non-structural proteins. The NS3 protein encodes a RNA triphosphatase within its helicase domain. It uses the helicase ATP hydrolysis site to remove the γ-phosphate from the 5′ end of the RNA. The N-terminal domain of the non-structural protein 5 has both the N7-methyltransferase and guanylyltransferase activities necessary for forming mature RNA cap structures. RNA binding affinity is reduced by the presence of ATP or GTP and enhanced by S-adenosyl methionine. This protein also encodes a 2′-O methyltransferase.
Once translated, the polyprotein is cleaved by a combination of viral and host proteases to release mature polypeptide products. Nevertheless, cellular post-translational modification is dependent on the presence of a poly-A tail; therefore this process is not host-dependent. Instead, the poly-protein contains an autocatalytic feature which automatically releases the first peptide, a virus specific enzyme. This enzyme is then able to cleave the remaining poly-protein into the individual products. One of the products cleaved is a RNA-dependent RNA polymerase, responsible for the synthesis of a negative-sense RNA molecule. Consequently, this molecule acts as the template for the synthesis of the genomic progeny RNA.
Flavivirus genomic RNA replication occurs on rough endoplasmic reticulum membranes in membranous compartments. New viral particles are subsequently assembled. This occurs during the budding process which is also responsible for the accumulation of the envelope and cell lysis.
A G protein-coupled receptor kinase 2 appears to be important in entry and replication for several viruses in Flaviviridae.
Humans, mammals, mosquitoes, and ticks serve as the natural host. Transmission routes are zoonosis and bite.
| Genus | Host details | Tissue tropism | Entry details | Release details | Replication site | Assembly site | Transmission |
| Flavivirus | Humans; mammals; mosquitoes; ticks | Epithelium: skin; epithelium: kidney; epithelium: intestine; epithelium: testes | Clathrin-mediated endocytosis | Secretion | Cytoplasm | Cytoplasm | Zoonosis; arthropod bite |
RNA secondary structure elements
The positive sense RNA genome of Flavivirus contains 5' and 3' untranslated regions.5'UTR
The 5'UTRs are 95–101 nucleotides long in Dengue virus. There are two conserved structural elements in the Flavivirus 5'UTR, a large stem loop and a short stem loop. SLA folds into a Y-shaped structure with a side stem loop and a small top loop. SLA is likely to act as a promoter, and is essential for viral RNA synthesis. SLB is involved in interactions between the 5'UTR and 3'UTR which result in the cyclisation of the viral RNA, which is essential for viral replication.3'UTR
The 3'UTRs are typically 0.3–0.5 kb in length and contain a number of highly conserved secondary structures which are conserved and restricted to orthoflaviviruses. The majority of analysis has been carried out using West Nile virus to study the function the 3'UTR.Currently 8 secondary structures have been identified within the 3'UTR of WNV and are SL-I, SL-II, SL-III, SL-IV, DB1, DB2 and CRE. Some of these secondary structures have been characterised and are important in facilitating viral replication and protecting the 3'UTR from 5' endonuclease digestion. Nuclease resistance protects the downstream 3' UTR RNA fragment from degradation and is essential for virus-induced cytopathicity and pathogenicity.
- SL-II
- SL-IV
- DB1/DB2
- CRE