Flavivirus

Flavivirus is a genus of viruses in the family Flaviviridae. This genus includes the West Nile virus, dengue virus, tick-borne encephalitis virus, yellow fever virus, and several other viruses which may cause encephalitis.

Flaviviruses are named from the yellow fever virus, the type virus for the family; the word "flavus" means "yellow" in Latin. The name "yellow fever" originated from its propensity to cause yellow jaundice in victims.

Flaviviruses share several common aspects: common size (40-65 nm), symmetry (enveloped, icosahedral nucleocapsid), nucleic acid (positive-sense, single-stranded RNA of approximately 10,000â€"11,000 bases), and appearance in the electron microscope.

Most of these viruses are transmitted by the bite from an infected arthropod (mosquito or tick) and hence, classified as arboviruses. Human infections with these viruses are typically incidental, as humans are unable to replicate the virus to high enough titres to reinfect arthropods needed to continue the virus life cycle â€" man is a dead end host. The exceptions to this are yellow fever and dengue viruses, which still require mosquito vectors, but are well-enough adapted to humans as to not necessarily depend upon animal hosts (although both continue to have important animal transmission routes as well).

Other virus transmission routes for arboviruses include handling infected animal carcasses, blood transfusion, child birth and through consumption of unpasteurised milk products. The transmission from animals to humans without an intermediate vector arthropod is thought to be unlikely. For example, early tests with yellow fever showed that the disease is not contagious.

The known non-arboviruses of the flavivirus family either reproduce in arthropods or vertebrates, but not both.

Replication

Flaviviruses have a (+) sense RNA genome and 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 (poly-A) tail. This feature allows the virus to exploit cellular apparatus to synthesise 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. In general, the genome encodes 3 structural proteins (Capsid, prM, and Envelope) and 8 non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, NS5 and NS5B). The genomic RNA is modified at the 5′ end of positive-strand genomic RNA with a cap-1 structure (me⁷-GpppA-me²).

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 (NS5) 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 polyprotein contains an autocatalytic feature which automatically releases the first peptide, a virus specific enzyme. This enzyme is then able to cleave the remaining polyprotein into the individual products. One of the products cleaved is a polymerase, responsible for the synthesis of a (-) 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 (also known as ADRBK1) appears to be important in entry and replication for several Flaviviridae.

RNA secondary structure elements

The (+) sense RNA genome of Flavivirus contains 5' and 3' untranslated regions (UTRs).

5'UTR

The 5'UTRs are 95â€"101 nucleotides long in Dengue virus. 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. 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 0.3â€"0.5 kb in length and contain a number of highly conserved secondary structures which are conserved and restricted to the flavivirus family. The majority of analysis has been carried out using West Nile virus (WNV) to study the function the 3'UTR.

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. 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-II has been suggested to contribute to nuclease resistance. It may be related to another hairpin loop identified in the 5'UTR of the Japanese encephalitis virus (JEV) genome. The JEV hairpin is significantly over-represented upon host cell infection and it has been suggested that the hairpin structure may play a role in regulating RNA synthesis.

• 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.

• 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%.

• 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". 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. 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.

Evolution

The flaviviruses can be divided into 2 clades: one with the vector borne viruses and the other with no known vector. The vector clade can be subdivided into a mosquito borne clade and a tick borne clade. These groups can be divided again.

The mosquito group can be divided into two branches: one branch contains the 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 which are associated with haemorrhagic disease in humans. These tend to have Aedes species as vectors and primate hosts.

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.

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.

It seems likely that tick transmission may have been derived from a mosquito borne group.

Species

Tick-borne viruses

• Mammalian tick-borne virus group
  • Alkhurma virus (ALKV)
  • Deer tick virus (DT)
  • Gadgets Gully virus (GGYV)
  • Kadam virus (KADV)
  • Karshi virus
  • Kyasanur Forest disease virus (KFDV)
  • Langat virus (LGTV)
  • Louping ill virus (LIV)
  • Omsk hemorrhagic fever virus (OHFV)
  • Powassan virus (POWV)
  • Royal Farm virus (RFV)
  • Sokuluk virus (SOKV)
  • Tick-borne encephalitis virus (TBEV)
  • Turkish sheep encephalitis virus (TSE)
• 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
  • Aedes flavivirus
  • Barkedji virus
  • Calbertado virus
  • Cell fusing agent virus
  • Chaoyang virus
  • Culex flavivirus
  • Culex theileri flavivirus
  • Donggang virus
  • Ilomantsi virus
  • Kamiti River virus
  • Lammi virus
  • Marisma mosquito virus
  • Nakiwogo virus
  • Nhumirim virus
  • Nounane virus
  • Spanish Culex flavivirus
  • Spanish Ochlerotatus flavivirus
  • Quang Binh virus
• Aroa virus group
  • Aroa virus (AROAV)
• Dengue virus group
  • Dengue virus (DENV)
  • Kedougou virus (KEDV)
• Japanese encephalitis virus group
  • Bussuquara virus
  • Cacipacore virus (CPCV)
  • Koutango virus (KOUV)
  • Ilheus virus (ILHV)
  • Japanese encephalitis virus (JEV)
  • Murray Valley encephalitis virus (MVEV)
  • Rocio virus (ROCV)
  • St. Louis encephalitis virus (SLEV)
  • Usutu virus (USUV)
  • West Nile virus (WNV)
  • Yaounde virus (YAOV)
• Kokobera virus group
  • Kokobera virus (KOKV)
• Ntaya virus group
  • Bagaza virus (BAGV)
  • Duck egg drop syndrome virus (BYDV)
  • Ilheus virus (ILHV)
  • Jiangsu virus (JSV)
  • Israel turkey meningoencephalomyelitis virus (ITV)
  • Ntaya virus (NTAV)
  • Tembusu virus (TMUV)
• Spondweni virus group
  • Zika virus (ZIKV)
• Yellow fever virus group
  • Banzi virus (BANV)
  • Bouboui virus (BOUV)
  • Edge Hill virus (EHV)
  • Jugra virus (JUGV)
  • Saboya virus (SABV)
  • Sepik virus (SEPV)
  • Uganda S virus (UGSV)
  • Wesselsbron virus (WESSV)
  • Yellow fever virus (YFV)

Viruses with no known arthropod vector

• 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

• Soybean cyst nematode virus 5

Vaccines

The successful yellow fever 17D vaccine, introduced in 1937, produced dramatic reductions in epidemic activity. Effective killed 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 killed 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. 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. A tetravalent chimeric vaccine that splices structural genes of the four dengue viruses onto a 17D yellow fever backbone is in Phase III clinical testing.

References

• Kuno G, Chang GJ, Tsuchiya KR, Karabatsos N, Cropp CB (Jan 1998). "Phylogeny of the genus Flavivirus". J Virol 72 (1): 73â€"83. PMC 109351. PMID 9420202. 
• Zanotto PM; Gould, Ernest A.; Gao, George F.; Harvey, Paul H.; Holmes, Edward C. (Jan 1996). "Population dynamics of flaviviruses revealed by molecular phylogenies". Proc Natl Acad Sci U S A. 93 (2): 548â€"53. Bibcode:1996PNAS...93..548Z. doi:10.1073/pnas.93.2.548. PMC 40088. PMID 8570593. 
• Molecular Biology of the Flavivirus. - Matthias Kalitzky, Taylor & Francis Ltd 2005 Oct 5; ISBN 1-904933-22-X
• Molecular Virology and Control of Flaviviruses. - Pei-Yong Shi, Caister Academic Press; ISBN 978-1-904455-92-9
• Architects of Assembly: roles of Flaviviridae nonstructural proteins in virion morphogenesis. -Catherine L. Murray, Christopher T. Jones, and Charles M. Rice | PMCID: PMC2764292

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
• 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