Flavivirus

Viruses in Flavivirus are enveloped, with icosahedral and spherical geometries. The diameter is around 50 nm. Genomes are linear positive-sense RNA and non-segmented, around 10–11kb in length.[7]

Entry into the host cell is achieved by attachment of the viral envelope protein E to host receptors, which mediates clathrin-mediated endocytosis. Replication follows the positive stranded RNA virus replication model. Positive stranded RNA virus transcription is the method of transcription. Humans, mammals, mosquitoes, and ticks serve as the natural host. Transmission routes are zoonosis and bite.[7]

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 7 non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, NS5).[8] 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.[9] 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.[10] 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.[11]

Flavivirus 3'UTR stem loop IV
Predicted secondary structure of the Flavivirus 3'UTR stem loop IV
Identifiers
Symbol	Flavivirus_SLIV
Rfam	RF01415
Other data
RNA type	Cis-reg
Domain(s)	Flaviviridae
SO	0005836
PDB structures	PDBe

Flavivirus DB element
Predicted secondary structure of the Flavivirus DB element
Identifiers
Symbol	Flavivirus_DB
Rfam	RF00525
Other data
RNA type	Cis-reg
Domain(s)	Flaviviridae
SO	0000233
PDB structures	PDBe

Flavivirus 3' UTR cis-acting replication element (CRE)
Predicted secondary structure of the Flavivirus 3' UTR cis-acting replication element (CRE)
Identifiers
Symbol	Flavi_CRE
Alt. Symbols	Flavi_pk3
Rfam	RF00185
Other data
RNA type	Cis-reg
Domain(s)	Flaviviridae
SO	0000205
PDB structures	PDBe

Japanese encephalitis virus (JEV) hairpin structure
Predicted secondary structure of the Japanese encephalitis virus (JEV) hairpin structure
Identifiers
Symbol	JEV_hairpin
Rfam	RF00465
Other data
RNA type	Cis-reg
Domain(s)	Flaviviridae
SO	0000233
PDB structures	PDBe

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

Subgenomic flavivirus RNA (sfRNA) is an extension of the 3' UTR and has been demonstrated to play a role in flavivirus replication and pathogenesis.[23] sfRNA is produced by incomplete degradation of genomic viral RNA by the host cells 5'-3' exoribonuclease 1 (XRN1).[24] As the XRN1 degrades viral RNA, it stalls at stemloops formed by the secondary structure of the 5' and 3' UTR.[25] This pause results in an undigested fragment of genome RNA known as sfRNA. sfRNA influences the life cycle of the flavivirus in a concentration dependent manner. Accumulation of sfRNA causes (1) antagonization of the cell's innate immune response, thus decreasing host defense against the virus[26] (2) inhibition of XRN1 and Dicer activity to modify RNAi pathways that destroy viral RNA[27] (3) modification of the viral replication complex to increase viral reproduction.[28] Overall, sfRNA is implied in multiple pathways that compromise host defenses and promote infection by flaviviruses.

The flaviviruses can be divided into 2 clades: one with the vector borne viruses and the other with no known vector.[29] The vector clade in turn can be subdivided into a mosquito-borne clade and a tick-borne clade. These groups can be divided again.[30]

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.[31]

A partial genome of a flavivirus has been found in the sea spider Endeis spinosa.[32] The sequences are related to those in the insect specific flaviviruses. It is not presently clear how this sequence fits into the evolution of this group of viruses.

Estimates of divergence times have been made for several of these viruses.[33] 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.

Phylogenetic studies of the West Nile Virus have shown that it emerged as a distinct virus around 1000 years ago.[34] This initial virus developed into two distinct lineages, lineage 1 and its multiple profiles is the source of the epidemic transmission in Africa and throughout the world. Lineage 2 was considered an Africa zoonosis. However, in 2008, lineage 2, previously only seen in horses in sub-Saharan Africa and Madagascar, began to appear in horses in Europe, where the first known outbreak affected 18 animals in Hungary in 2008.[35] Lineage 1 West Nile virus was detected in South Africa in 2010 in a mare and her aborted fetus; previously, only lineage 2 West Nile virus had been detected in horses and humans in South Africa.[36] A 2007 fatal case in a killer whale in Texas broadened the known host range of West Nile virus to include cetaceans.[37]

Omsk haemorrhagic fever virus appears to have evolved within the last 1000 years.[38] The viral genomes can be divided into 2 clades — A and B. Clade A has five genotypes and clade B has one. These clades separated about 700 years ago. This separation appears to have occurred in the Kurgan province. Clade A subsequently underwent division into clade C, D and E 230 years ago. Clade C and E appear to have originated in the Novosibirsk and Omsk Provinces respectively. The muskrat Ondatra zibethicus which is highly susceptible to this virus was introduced into this area in the 1930s.

The very successful yellow fever 17D vaccine, introduced in 1937, produced dramatic reductions in epidemic activity.

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.

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.[41][42] Dengvaxia is approved in five countries.[43]

• Kuno G, Chang GJ, Tsuchiya KR, Karabatsos N, Cropp CB (January 1998). "Phylogeny of the genus Flavivirus". J Virol. 72 (1): 73–83. PMC 109351. PMID 9420202.
• Zanotto, P. M.; Gould, E. A.; Gao, G. F.; Harvey, P. H.; Holmes, E. C. (1996). "Population dynamics of flaviviruses revealed by molecular phylogenies". Proceedings of the National Academy of Sciences. 93 (2): 548–553. Bibcode:1996PNAS...93..548Z. doi:10.1073/pnas.93.2.548. PMC 40088. PMID 8570593.
• Kalitzky, Matthias (2006). Molecular Biology of the Flavivirus. Wymondham: Horizon Bioscience. ISBN 978-1-904933-22-9.
• Shi, Pei-Yong (2012). Molecular Virology and Control of Flaviviruses. Norfolk, UK: Caister Academic Press. ISBN 978-1-904455-92-9.
• Murray, Catherine L.; Jones, Christopher T.; Rice, Charles M. (2008). "Architects of assembly: roles of Flaviviridae non-structural proteins in virion morphogenesis". Nature Reviews Microbiology. 6 (9): 699–708. doi:10.1038/nrmicro1928. PMC 2764292. PMID 18587411.

• 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