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Flavivirus

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Flavivirus
A TEM micrograph of the yellow fever virus
Virus classification
Group:
Group IV ((+)ssRNA)
Family:
Flaviviridae
Genus:
Flavivirus
Type species
Yellow fever virus [1]
Species

(see list in article)

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, Zika virus and several other viruses which may cause encephalitis.[2]

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.[3]

Flaviviruses share several common aspects: common size (40–65 nm), symmetry (enveloped, icosahedral nucleocapsid), nucleic acid (positive-sense, single-stranded RNA around 10,000–11,000 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 usually unable to replicate the virus to high enough titers to reinfect the arthropods needed to continue the virus lifecycle – man is then a dead end host. The exceptions to this are the yellow fever, dengue, and zika viruses, which still require mosquito vectors, but are well-enough adapted to humans as to not necessarily depend upon animal hosts (although they 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 reproduce in either arthropods or vertebrates, but not both, with one odd member of the genus affecting a nematode.

Taxonomy

Group: ssRNA(+)

Order: Unassigned

[4]

Structure

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.[5]

Genus Structure Symmetry Capsid Genomic Arrangement Genomic Segmentation
Flavivirus Icosahedral-like Pseudo T=3 Enveloped Linear Monopartite

Life Cycle

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.[5]

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

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) [citation needed]. 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.[6] 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.[7]

RNA secondary structure elements

Flavivirus 3'UTR stem loop IV
Predicted secondary structure of the Flavivirus 3'UTR stem loop IV
Identifiers
SymbolFlavivirus_SLIV
RfamRF01415
Other data
RNA typeCis-reg
Domain(s)Flaviviridae
SOSO:0005836
PDB structuresPDBe
Flavivirus DB element
Predicted secondary structure of the Flavivirus DB element
Identifiers
SymbolFlavivirus_DB
RfamRF00525
Other data
RNA typeCis-reg
Domain(s)Flaviviridae
SOSO:0000233
PDB structuresPDBe
Flavivirus 3' UTR cis-acting replication element (CRE)
Predicted secondary structure of the Flavivirus 3' UTR cis-acting replication element (CRE)
Identifiers
SymbolFlavi_CRE
Alt. SymbolsFlavi_pk3
RfamRF00185
Other data
RNA typeCis-reg
Domain(s)Flaviviridae
SOSO:0000205
PDB structuresPDBe
Japanese encephalitis virus (JEV) hairpin structure
Predicted secondary structure of the Japanese encephalitis virus (JEV) hairpin structure
Identifiers
SymbolJEV_hairpin
RfamRF00465
Other data
RNA typeCis-reg
Domain(s)Flaviviridae
SOSO:0000233
PDB structuresPDBe

The (+) 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.[8] 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.[8][9] SLA is likely to act as a promoter, and is essential for viral RNA synthesis.[10][11] 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.[12]

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 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.[13][14] 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.[14] It may be related to another hairpin loop identified in the 5'UTR of the Japanese encephalitis virus (JEV) genome.[15] 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%.[13]

  • 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".[16] 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.[17] 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.[18]

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.[19] sfRNA is produced by incomplete degredation of genomic viral RNA by the host cells 5'-3' exoribonuclease-1 (XRN1).[20] As the XRN1 degrades viral RNA, it stalls at stemloops formed by the secondary structure of the 5' and 3' UTR.[21] 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[22] (2) inhibition of XRN1 and Dicer activity to modify RNAi pathways that destroy viral RNA[23] (3) modification of the viral replication complex to increase viral reproduction.[24] Overall, sfRNA is implied in multiple pathways that compromise host defenses and promote infection by flaviviruses.

Evolution

The flaviviruses can be divided into 2 clades: one with the vector borne viruses and the other with no known vector.[25] The vector clade in turn can be subdivided into a mosquito borne clade and a tick borne clade. These groups can be divided again.[26]

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.[27]

A partial genome of a flavivirus has been found in the sea spider Endeis spinosa.[28] 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.

Species

Tick-borne viruses

Mosquito-borne viruses

  • Without known vertebrate host

Viruses with no known arthropod vector

Non vertebrate viruses

Viruses known only from sequencing

Vaccines

The very 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.[2]

References

  1. ^ International Committee on Taxonomy of Viruses (20 March 2010). "ICTV 2009 Master Species List Version 4".
  2. ^ a b Shi, P-Y (editor) (2012). Molecular Virology and Control of Flaviviruses. Caister Academic Press. ISBN 978-1-904455-92-9. {{cite book}}: |author= has generic name (help)
  3. ^ The earliest mention of "yellow fever" appears in a manuscript of 1744 by Dr. John Mitchell of Virginia; copies of the manuscript were sent to Mr. Cadwallader Colden, a physician in New York, and to Dr. Benjamin Rush of Philadelphia; the manuscript was eventually reprinted in 1814. See:
    (Dr. John Mitchell) (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. The term "yellow fever" appears on p. 186. On p. 188, Mitchell mentions "… the distemper was what is generally called the yellow fever in America." However, on pages 191–192, he states "… I shall consider the cause of the yellowness which is so remarkable in this distemper, as to have given it the name of the Yellow Fever."
    Dr. Mitchell misdiagnosed the disease that he observed and treated, and the disease was probably Weil's disease or hepatitis. See: Saul Jarcho (1957) "John Mitchell, Benjamin Rush, and Yellow fever". Bulletin of the History of Medicine, 31 (2) : 132–6.
  4. ^ ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015.
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  21. ^ Funk, Anneke; Truong, Katherine; Nagasaki, Tomoko; Torres, Shessy; Floden, Nadia; Melian, Ezequiel Balmori; Edmonds, Judy; Dong, Hongping; Shi, Pei-Yong (2010-11-01). "RNA Structures Required for Production of Subgenomic Flavivirus RNA". Journal of Virology. 84 (21): 11407–11417. doi:10.1128/JVI.01159-10. ISSN 0022-538X. PMC 2953152. PMID 20719943.
  22. ^ Chang, Ruey-Yi; Hsu, Ta-Wen; Chen, Yen-Lin; Liu, Shu-Fan; Tsai, Yi-Jer; Lin, Yun-Tong; Chen, Yi-Shiuan; Fan, Yi-Hsin (2013-09-27). "Japanese encephalitis virus non-coding RNA inhibits activation of interferon by blocking nuclear translocation of interferon regulatory factor 3". Veterinary Microbiology. 166 (1–2): 11–21. doi:10.1016/j.vetmic.2013.04.026.
  23. ^ Moon, Stephanie L.; Anderson, John R.; Kumagai, Yutaro; Wilusz, Carol J.; Akira, Shizuo; Khromykh, Alexander A.; Wilusz, Jeffrey (2012-11-01). "A noncoding RNA produced by arthropod-borne flaviviruses inhibits the cellular exoribonuclease XRN1 and alters host mRNA stability". RNA. 18 (11): 2029–2040. doi:10.1261/rna.034330.112. ISSN 1355-8382. PMC 3479393. PMID 23006624.
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  27. ^ Cook S, Holmes EC (2006). "A multigene analysis of the phylogenetic relationships among the flaviviruses (Family: Flaviviridae) and the evolution of vector transmission". Arch Virol. 151 (2): 309–325. doi:10.1007/s00705-005-0626-6. PMID 16172840.
  28. ^ Conway MJ (2015) Identification of a flavivirus sequence in a marine arthropod. PLoS One 10(12):e0146037. doi: 10.1371/journal.pone.0146037
  29. ^ Bekal S, Domier LL, Gonfa B, McCoppin NK, Lambert KN, Bhalerao K. "A novel flavivirus in the soybean cyst nematode". PubMed. doi:10.1099/vir.0.060889-0.{{cite journal}}: CS1 maint: multiple names: authors list (link)
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