Flavivirus
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Flavivirus | |
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A Yellow fever virus
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Zika virus viral envelope model, colored by chains, PDB entry 5ire[2] | |
Virus classification | |
(unranked): | Virus |
Realm: | Riboviria |
Kingdom: | Orthornavirae |
Phylum: | Kitrinoviricota |
Class: | Flasuviricetes |
Order: | Amarillovirales |
Family: | Flaviviridae |
Genus: | Flavivirus |
Species[1] | |
Flavivirus, renamed Orthoflavivirus in 2023,
Flaviviruses 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.[8]
Flaviviruses share several common aspects: common size (40–65 nm), symmetry (
Most of these viruses are primarily transmitted by the bite from an infected
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.[9]
Structure
Flaviviruses are enveloped and spherical and have icosahedral geometries with a pseudo T=3 symmetry. The virus particle diameter is around 50 nm.[10]
Genome
Flaviviruses have positive-sense, single-stranded RNA genomes which are non-segmented and around 10–11 kbp in length.[10] In general, the genome encodes three structural proteins (Capsid, prM, and Envelope) and seven non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, NS5).[11] The genomic RNA is modified at the 5′ end of positive-strand genomic RNA with a cap-1 structure (me7-GpppA-me2).[12]
Life cycle
Flaviviruses replicate in the
Cellular RNA cap structures are formed via the action of an
Once
Flavivirus genomic RNA replication occurs on
A G protein-coupled receptor kinase 2 (also known as ADRBK1) appears to be important in entry and replication for several viruses in Flaviviridae.[14]
Humans, mammals, mosquitoes, and ticks serve as the natural host. Transmission routes are zoonosis and bite.[10]
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 (UTRs).
5'UTR
The 5'UTRs are 95–101 nucleotides long in Dengue virus.[15] There are two conserved structural elements in the Flavivirus 5'UTR, a large stem loop (SLA) and a short stem loop (SLB). SLA folds into a Y-shaped structure with a side stem loop and a small top loop.[15][16] SLA is likely to act as a promoter, and is essential for viral RNA synthesis.[17][18] 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.[19]
3'UTR
The 3'UTRs are typically 0.3–0.5 kb in length and contain a number of highly conserved
Currently 8 secondary structures have been identified within the 3'UTR of WNV and are (in the order in which they are found with the 3'UTR) SL-I, SL-II, SL-III, SL-IV, DB1, DB2 and CRE.[20][21] 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.[citation needed]
- SL-II
SL-II has been suggested to contribute to nuclease resistance.
- SL-IV
This secondary structure is located within the 3'UTR of the genome of Flavivirus upstream of the DB elements. The function of this conserved structure is unknown but is thought to contribute to ribonuclease resistance.[citation needed]
- DB1/DB2
These two conserved secondary structures are also known as pseudo-repeat elements. They were originally identified within the genome of Dengue virus and are found adjacent to each other within the 3'UTR. They appear to be widely conserved across the Flaviviradae. These DB elements have a secondary structure consisting of three helices and they play a role in ensuring efficient translation. Deletion of DB1 has a small but significant reduction in translation but deletion of DB2 has little effect. Deleting both DB1 and DB2 reduced translation efficiency of the viral genome to 25%.[20]
- CRE
CRE is the Cis-acting replication element, also known as the 3'SL RNA elements, and is thought to be essential in viral replication by facilitating the formation of a "replication complex".[23] Although evidence has been presented for an existence of a pseudoknot structure in this RNA, it does not appear to be well conserved across flaviviruses.[24] Deletions of the 3' UTR of flaviviruses have been shown to be lethal for infectious clones.
Conserved hairpin cHP
A conserved hairpin (cHP) structure was later found in several Flavivirus genomes and is thought to direct translation of capsid proteins. It is located just downstream of the AUG start codon.[25]
The role of RNA secondary structures in sfRNA production
Subgenomic flavivirus RNA (sfRNA) is an extension of the 3' UTR and has been demonstrated to play a role in flavivirus replication and pathogenesis.
Evolution
The flaviviruses can be divided into two clades: one with vector-borne viruses and the other with no known vector.[32] The vector clade, in turn, can be subdivided into a mosquito-borne clade and a tick-borne clade. These groups can be divided again.[33]
The mosquito group can be divided into two branches: one branch contains neurotropic viruses, often associated with encephalitic disease in humans or livestock. This branch tends to be spread by Culex species and to have bird reservoirs. The second branch is the non-neurotropic viruses associated with human haemorrhagic disease. These tend to have Aedes species as vectors and primate hosts.[citation needed]
The tick-borne viruses also form two distinct groups: one is associated with seabirds and the other – the tick-borne encephalitis complex viruses – is associated primarily with rodents.[citation needed]
The viruses that lack a known vector can be divided into three groups: one closely related to the mosquito-borne viruses, which is associated with bats; a second, genetically more distant, is also associated with bats; and a third group is associated with rodents.[citation needed]
Evolutionary relationships between endogenised viral elements of Flaviviruses and contemporary flaviviruses using maximum likelihood approaches have identified that arthropod-vectored flaviviruses likely emerged from an arachnid source.[34] This contradicts earlier work with a smaller number of extant viruses showing that the tick-borne viruses emerged from a mosquito-borne group.[35]
Several partial and complete genomes of flaviviruses have been found in aquatic invertebrates such as the sea spider Endeis spinosa[36] and several crustaceans and cephalopods.[37] These sequences appear to be related to those in the insect-specific flaviviruses and also the Tamana bat virus groupings. While it is not presently clear how aquatic flaviviruses fit into the evolution of this group of viruses, there is some evidence that one of these viruses, Wenzhou shark flavivirus, infects both a crustacean (Portunus trituberculatus) Pacific spadenose shark (Scoliodon macrorhynchos) shark host,[38][37] indicating an aquatic arbovirus life cycle.
Estimates of divergence times have been made for several of these viruses.[39] The origin of these viruses appears to be at least 9400 to 14,000 years ago. The Old World and New World dengue strains diverged between 150 and 450 years ago. The European and Far Eastern tick-borne encephalitis strains diverged about 1087 (1610–649) years ago. European tick-borne encephalitis and louping ill viruses diverged about 572 (844–328) years ago. This latter estimate is consistent with historical records. Kunjin virus diverged from West Nile virus approximately 277 (475–137) years ago. This time corresponds to the settlement of Australia from Europe. The Japanese encephalitis group appears to have evolved in Africa 2000–3000 years ago and then spread initially to South East Asia before migrating to the rest of Asia.
Omsk haemorrhagic fever virus appears to have evolved within the last 1000 years.
Taxonomy
Species
In the genus Flavivirus there are 53 defined species:[45]
- Apoi virus
- Aroa virus
- Bagaza virus
- Banzi virus
- Bouboui virus
- Bukalasa bat virus
- Cacipacore virus
- Carey Island virus
- Cowbone Ridge virus
- Dakar bat virus
- Dengue virus
- Edge Hill virus
- Entebbe bat virus
- Gadgets Gully virus
- Ilheus virus
- Israel turkey meningoencephalomyelitis virus
- Japanese encephalitis virus
- Jugra virus
- Jutiapa virus
- Kadam virus
- Kedougou virus
- Kokobera virus
- Koutango virus
- Kyasanur Forest disease virus
- Langat virus
- Louping ill virus
- Meaban virus
- Modoc virus
- Montana myotis leukoencephalitis virus
- Murray Valley encephalitis virus
- Ntaya virus
- Omsk hemorrhagic fever virus
- Phnom Penh bat virus
- Powassan virus
- Rio Bravo virus
- Royal Farm virus
- Saboya virus
- Saint Louis encephalitis virus
- Sal Vieja virus
- San Perlita virus
- Saumarez Reef virus
- Sepik virus
- Tembusu virus
- Tick-borne encephalitis virus
- Tyuleniy virus
- Uganda S virus
- Usutu virus
- Wesselsbron virus
- West Nile virus
- Yaounde virus
- Yellow fever virus
- Yokose virus
- Zika virus
Sorted by vector
Species and strains sorted by vectors:
Tick-borne viruses
Mammalian tick-borne virus group
- Greek goat encephalitis virus (GGEV)
- Kadam virus (KADV)
- Krasnodar virus (KRDV)
- Mogiana tick virus (MGTV)
- Ngoye virus (NGOV)
- Sokuluk virus (SOKV)
- Spanish sheep encephalomyelitis virus (SSEV)
- Turkish sheep encephalitis virus (TSE)
- Tick-borne encephalitis virus serocomplex
- Absettarov virus
- Deer tick virus (DT)
- Gadgets Gully virus (GGYV)
- Karshi virus
- Kyasanur Forest disease virus(KFDV)
- Alkhurma hemorrhagic fever virus(ALKV)
- Langat virus (LGTV)
- Louping ill virus(LIV)
- Omsk hemorrhagic fever virus(OHFV)
- Powassan virus (POWV)
- Royal Farm virus (RFV)
- Tick-borne encephalitis virus (TBEV)
Seabird tick-borne virus group
- Kama virus (KAMV)
- Meaban virus (MEAV)
- Saumarez Reef virus (SREV)
- Tyuleniy virus (TYUV)
Mosquito-borne viruses
- Without known vertebrate host
- Cell fusing clade
- Aedes galloisi flavivirus
- Barkedji virus
- Calbertado virus
- Chaoyang virus
- Culex flavivirus
- Culex theileri flavivirus
- Culiseta flavivirus
- Donggang virus
- Hanko virus
- Ilomantsi virus
- Kamiti River virus
- Lammi virus
- Marisma mosquito virus
- Nakiwogo virus
- Nhumirim virus
- Nienokoue virus
- Nounané virus
- Palm Creek virus
- Panmunjeom flavivirus
- Quang Binh virus
- Aroa virus group
- Aroa virus (AROAV)
- Bussuquara virus (BSQV)
- Iguape virus (IGUV)
- Naranjal virus (NJLV)
- Dengue virus group
- Dengue virus (DENV)
- Kedougou virus (KEDV)[46][47]
- Japanese encephalitis virus group
- Cacipacore virus (CPCV)
- Koutango virus (KOUV)
- Kunjin virus
- Ilheus virus (ILHV)
- Japanese encephalitis virus(JEV)
- Murray Valley encephalitis virus (MVEV)
- St. Louis encephalitis virus(SLEV)
- Usutu virus (USUV)
- West Nile virus (WNV)
- Yaounde virus (YAOV)
- Kokobera virus group
- Kokobera virus (KOKV)
- New Mapoon virus (NMV)
- Stratford virus (STRV)
- Ntaya virus group
- Bagaza virus (BAGV)
- Baiyangdian virus (BYDV)
- Duck egg drop syndrome virus (DEDSV)
- Ilheus virus (ILHV)
- Israel turkey meningoencephalomyelitis virus (ITV)
- Jiangsu virus (JSV)
- Layer flavivirus
- Ntaya virus (NTAV)
- Rocio virus(ROCV)
- Sitiawan virus (STWV)
- T'Ho virus
- Tembusu virus (TMUV)
- Spondweni virus group
- Spondweni virus (SPOV)
- Zika virus (ZIKV)
- Yellow fever virus group
- Banzi virus (BANV)
- Bamaga virus (BGV)
- Bouboui virus (BOUV)
- Edge Hill virus (EHV)
- Fitzroy river virus
- Jugra virus (JUGV)
- Saboya virus (SABV)
- Sepik virus (SEPV)
- Uganda S virus (UGSV)
- Wesselsbron virus (WESSV)
- Yellow fever virus(YFV)
- Others
Viruses with no known arthropod vector
- Tamana bat virus (TABV)
- Entebbe virus group
- Entebbe bat virus (ENTV)
- Yokose virus (YOKV)
- Modoc virus group
- Apoi virus (APOIV)
- Cowbone Ridge virus (CRV)
- Jutiapa virus (JUTV)
- Modoc virus (MODV)
- Sal Vieja virus (SVV)
- San Perlita virus (SPV)
- Rio Bravo virus group
- Bukalasa bat virus (BBV)
- Carey Island virus (CIV)
- Dakar bat virus (DBV)
- Montana myotis leukoencephalitis virus (MMLV)
- Phnom Penh bat virus (PPBV)
- Rio Bravo virus (RBV)
Non vertebrate viruses
- Assam virus
- Bamaga virus[48]
- Crangon crangon flavivirus[49]
- Cuacua virus
- Donggang virus
- Firefly squid flavivirus[49]
- Gammarus chevreuxi flavivirus[49]
- Gammarus pulex flavivirus[49]
- Karumba virus (KRBV)
- Hanko virus
- Haslams Creek virus
- Mac Peak virus (McPV)
- Marisma mosquito virus
- Mediterranean Ochlerotatus flavivirus
- Menghai flavivirus
- Nakiwogo virus (NAKV)
- Nanay virus
- Nounané virus
- Ochlerotatus caspius flavivirus
- Palm Creek virus
- Parramatta River virus
- Southern Pygmy squid flavivirus[49]
- Soybean cyst nematode virus 5[9]
- Xishuangbanna Aedes flavivirus
Viruses known only from sequencing
Vaccines
The very successful yellow fever 17D vaccine, introduced in 1937, produced dramatic reductions in epidemic activity.[citation needed]
Effective inactivated Japanese encephalitis and Tick-borne encephalitis vaccines were introduced in the middle of the 20th century. Unacceptable adverse events have prompted change from a mouse-brain inactivated Japanese encephalitis vaccine to safer and more effective second generation Japanese encephalitis vaccines. These may come into wide use to effectively prevent this severe disease in the huge populations of Asia—North, South and Southeast.[citation needed]
The dengue viruses produce many millions of infections annually due to transmission by a successful global mosquito vector. As mosquito control has failed, several dengue vaccines are in varying stages of development. CYD-TDV, sold under the trade name Dengvaxia, is a tetravalent chimeric vaccine that splices structural genes of the four dengue viruses onto a 17D yellow fever backbone.[50][51] Dengvaxia is approved in five countries.[52]
An alternate approach to the development of flavivirus vaccine vectors is based on the use of viruses that infect insects. Insect-specific flaviviruses, such as Binjari virus, are unable to replicate in vertebrate cells. Nevertheless, recombinant viruses in which structural protein genes (prME) of Binjari virus are exchanged with those of dengue virus, Zika virus, West Nile virus, yellow fever virus, or Japanese encephalitis virus replicate efficiently in insect cells where high titers of infectious virus particles are produced.
vaccine platform. ... These new vaccine platforms generated from insect-specific flaviviruses and alphaviruses represent affordable, efficient, and safe approaches to rapid development of infectious, attenuated vaccines against pathogens from these two virus families.[53]
References
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- Mitchell, John (written: 1744; reprinted: 1814) "Account of the Yellow fever which prevailed in Virginia in the years 1737, 1741, and 1742, in a letter to the late Cadwallader Colden, Esq. of New York, from the late John Mitchell, M.D.F.R.S. of Virginia", American Medical and Philosophical Register, 4: 181–215.
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Further reading
- Kuno G, Chang GJ, Tsuchiya KR, Karabatsos N, Cropp CB (January 1998). "Phylogeny of the genus Flavivirus". J Virol. 72 (1): 73–83. PMID 9420202.
- Zanotto PM, Gould EA, Gao GF, Harvey PH, Holmes EC (1996). "Population dynamics of flaviviruses revealed by molecular phylogenies". Proceedings of the National Academy of Sciences. 93 (2): 548–553. PMID 8570593.
- Kalitzky M (2006). Molecular Biology of the Flavivirus. Wymondham: Horizon Bioscience. ISBN 978-1-904933-22-9.
- Shi PY (2012). Molecular Virology and Control of Flaviviruses. Norfolk, UK: Caister Academic Press. ISBN 978-1-904455-92-9.
- Murray CL, Jones CT, Rice CM (2008). "Architects of assembly: roles of Flaviviridae non-structural proteins in virion morphogenesis". Nature Reviews Microbiology. 6 (9): 699–708. PMID 18587411.
External links
- MicrobiologyBytes: Flaviviruses
- Novartis Institute for Tropical Diseases (NITD) – Dengue Fever research at the Novartis Institute for Tropical Diseases (NITD)
- Dengueinfo.org – Depository of dengue virus genomic sequence data
- Viralzone: Flavivirus Archived 13 June 2010 at the Wayback Machine
- Virus Pathogen Database and Analysis Resource (ViPR): Flaviviridae
- Rfam entry for Flavivirus 3'UTR stem loop IV
- Rfam entry for Flavivirus DB element
- Rfam entry for Flavivirus 3' UTR cis-acting replication element (CRE)
- Rfam entry for the Japanese encephalitis virus (JEV) hairpin structure[permanent dead link]