Genus: Flavivirus

Genus: Flavivirus

Distinguishing features

The 5′ end of the genome possesses a type I cap (m7GpppAmp) not seen in viruses of the other genera. Most flaviviruses are transmitted to vertebrate hosts by arthropod vectors, mosquitoes or ticks, in which they replicate actively. Some flaviviruses transmit between rodents or bats without known arthropod vectors.



Virions are 50 nm in diameter and spherical in shape (Figure 1.Flavivirus). Two virus forms can be distinguished. Mature virions contain two virus encoded membrane-associated proteins, E and M. Intracellular immature virions contain the precursor prM, instead of M, which is proteolytically cleaved during maturation (Stadler et al., 1997). In certain instances, partially mature/immature forms are also released from infected cells. The virion structures of dengue virus (DENV) and West Nile virus (WNV) have been determined by X-ray crystallography (Kuhn et al., 2002, Mukhopadhyay et al., 2003). The envelope protein, E, is a dimeric, rod-shaped molecule that is oriented parallel to the membrane and does not form spike-like projections in its neutral pH conformation (Yu et al., 2008). Image reconstructions from cryo-electron micrographs (Figure 1.Flavivirus) have shown that the virion envelope has icosahedral symmetry, in which E protein dimers are organized in a herringbone-like arrangement.

Figure 1.Flavivirus. Three-dimensional cryo-electron microscopic reconstructions of immature (left) and mature (right) particles of an isolate of dengue virus (courtesy of M. Rossmann). Shown is a surface rendering of immature dengue virus at 12.5A resolution (left) and mature DENV at 10A resolution (right). The viruses are depicted to scale, but not coloured to scale. Triangles outline one icosahedral unit.

Physicochemical and physical properties

Virion Mr has not been precisely determined. Mature virions sediment at about 200S and have a buoyant density of about 1.19 g cm−3 in sucrose (Kokorev et al., 1976). Viruses are stable at slightly alkaline pH 8.0 but are readily inactivated at acidic pH, temperatures above 40 °C, organic solvents, detergents, ultraviolet light and gamma-irradiation.

Nucleic acid

The virion RNA of flaviviruses is a positive-sense infectious ssRNA of about 9.2-11.0 kb among different members of the genus. The 5′ end of the genome possesses a type I cap (m-7GpppAmp) where the A is followed by a highly conserved G nucleotide. The 3′ ends lack a terminal poly(A) tract and terminates with the conserved dinucleotide CU.


Virions contain three structural proteins: C (11 kDa), E (50 kDa), the major envelope protein, and either prM (26 kDa), in immature virions, or M (8 kDa), in mature virions. The E protein is the viral haemagglutinin, which mediates both receptor binding and acid pH-dependent fusion activity after uptake by receptor-mediated endocytosis. Seven nonstructural proteins are synthesized in infected cells: NS1 (46 kDa), NS2A (22 kDa), NS2B (14 kDa), NS3 (70 kDa), NS4A (16 kDa), NS4B (27 kDa) and NS5 (103 kDa). Some members appear to harbour sequences that induce a proportion of translating ribosomes to shift -1 nt and continue translating in the new reading frame to produce a 'transframe' fusion protein (Firth and Atkins 2009). When functionally utilized, this is referred to as programmed-1 ribosomal frameshifting (-1 PRF). NS1 has multiple forms and roles, with a cell-associated form functioning in viral RNA replication and a secreted form that regulates complement activation. One such form, a NS1′ protein, is the product of a −1 ribosomal frameshift and plays a role in viral neuroinvasiveness (Melian et al., 2010). The N-terminal one-third of NS1 forms the viral serine protease complex together with NS2B that is involved in processing the polyprotein. The C-terminal portion of NS3 contains an RNA helicase domain involved in RNA replication, as well as an RNA triphosphatase activity that is probably involved in formation of the 5′-terminal cap structure of the viral RNA. NS5 is the largest and most highly conserved protein that acts as the viral RdRp and also possesses methyltransferase activity involved in the modification of the viral cap structure.


Virions contain about 17% lipid by weight; lipids are derived from host cell membranes.


Virions contain about 9% carbohydrate by weight (glycolipids, glycoproteins); their composition and structure are dependent on the host cell (vertebrate or arthropod). N-glycosylation sites are present in the proteins prM (1 to 3 sites), E (0 to 2 sites) and NS1 (1 to 3 sites).

Genome organization and replication

The genomic RNA represents the only viral messenger RNA in infected cells. It consists of a single long ORF of more than 10,000 nt that codes for all structural and nonstructural proteins and is flanked by NCRs at the 5′- and 3′-terminal ends (Figure 2.Flavivirus).

Figure 2.Flavivirus. Flavivirus genome organization (not to scale) and polyprotein processing. The virion RNA is about 11 kb. At the top is the viral genome with the structural and nonstructural protein coding regions and the 5′- and 3′-NCRs. Boxes below the genome indicate viral proteins generated by the proteolytic processing cascade. P, H, and R symbols indicate the localization of the NS3 protease, the NS3 RNA helicase, and the NS5 RdRp domains, respectively.

Both the 5′-NCR and the 3′-NCR contain RNA sequence motifs that are involved in viral RNA translation, replication and possibly packaging. Although RNA secondary structure and function of some elements are conserved, sequence composition, length and exact localization can vary considerably between different members of the genus, in particular between tick-borne and mosquito-borne flaviviruses. In some cases, the 3′-NCR of tick-borne encephalitis virus, for example, contains an internal poly(A) tract. Viral infection induces dramatic rearrangements of cellular membrane structures within the perinuclear endoplasmic reticulum (ER) and causes the formation of ER-derived vesicular packets that most likely represent the sites of viral replication. After translation of the incoming genomic RNA, RNA replication begins with synthesis of complementary negative strands, which are then used as templates to produce additional genome-length positive-stranded molecules. These are synthesized by a semi-conservative mechanism involving replicative intermediates (containing double-stranded regions as well as nascent single-stranded molecules) and replicative forms (duplex RNA molecules). Translation usually starts at the first AUG of the ORF, but may also occur at a second in-frame AUG located 12 to 14 codons downstream in mosquito-borne flaviviruses. The polyprotein is processed by cellular proteases and the viral NS2B-NS3 serine protease to give rise to the mature structural and nonstructural proteins. Protein topology with respect to the ER and cytoplasm is determined by internal signal and stop-transfer sequences. Virus particles can first be observed in the rough endoplasmic reticulum, which is believed to be the site of virus assembly. These immature virions are then transported through the membrane systems of the host secretory pathway to the cell surface where exocytosis occurs. Shortly before virion release, the prM protein is cleaved by furin or a furin-like cellular protease to generate mature virions. Infected cells also release a non-infectious subviral particle that has a lower sedimentation coefficient than whole virus (70S vs. 200S) and exhibits haemagglutination activity.


All flaviviruses are serologically related, which can be demonstrated by binding assays such as ELISA and by haemagglutination-inhibition using polyclonal and monoclonal antibodies. Neutralization assays are more discriminating and have been used to identify more closely related Flavivirus serocomplexes (as indicated in Figure 1.Flaviviridae) although not down to the species level (see “List of species in the genus”). The envelope protein E is the major target for neutralizing antibodies and induces protective immunity. The E protein also induces flavivirus cross-reactive non-neutralizing antibodies. Antigenic sites involved in neutralization have been mapped to each of the three structural domains of the E protein. prM and NS1 proteins can also induce antibodies that protect infected animals from lethal infection.


Host range

Flaviviruses can infect a variety of vertebrate species and in many cases arthropods. Some viruses have a limited vertebrate host range (e.g., only primates), others can infect and replicate in a wide variety of species (mammals, birds, etc.). Arthropods are usually infected when they feed on a viraemic vertebrate host, but non-viraemic transmission between vectors has also been described for tick-borne flaviviruses. A new group of flaviviruses that appear only to infect mosquitoes is now recognized with the prototype, cell fusing agent virus, tentatively assigned to the genus Flavivirus. However, several more, highly genetically distinct insect-only flaviviruses have now been identified (Blitvich and Firth 2015) and will need to be considered as a possible separate group of viruses within the genus.


Most flaviviruses are arthropod-borne viruses with cycles of transmission from hematophagous arthropod vectors to vertebrate hosts. About 50% of known flaviviruses are mosquito-borne, 28% are tick-borne and the remainder transmit between rodents or bats without known arthropod vectors. For some flaviviruses, the transmission cycle has not yet been identified. In certain instances, flaviviruses can be transmitted to humans by blood products, organ transplantation, non-pasteurized milk or aerosols. Some tick-borne flaviviruses are known to be transmitted directly between ticks by a process known as non-viraemic transmission. In the arthropod vectors, the viruses may also be passed on trans-ovarially or vertically (mosquitoes, ticks) and trans-stadially (ticks). The mechanisms of virus transmission involving the insect-only flaviviruses may include vertical transmission, but other mechanisms need to be considered to explain the success with which these viruses appear to have dispersed globally.

Geographical distribution

Flaviviruses have a world-wide distribution but individual species are restricted to specific endemic or epidemic areas (e.g., yellow fever virus in tropical and subtropical regions of Africa and South America; dengue virus in tropical areas of Asia, Oceania, Africa, Australia and the Americas; Japanese encephalitis virus in Southeast Asia; tick-borne encephalitis virus in Europe and Northern Asia).


More than 50% of known flaviviruses have been associated with human disease, including many important human pathogens: yellow fever virus, dengue virus, Zika virus, Japanese encephalitis virus, West Nile virus and tick-borne encephalitis virus. The induced diseases may be associated with symptoms of the central nervous system (e.g., meningitis, encephalitis), fever, arthralgia, rash and haemorrhagic fever. Several flaviviruses are pathogenic for domestic or wild animals (turkey, pig, horse, sheep, dog, grouse, muskrat) and cause economically important diseases.

Species demarcation criteria

Species demarcation criteria in the genus include:

  • Nucleotide and deduced amino acid sequence data.
  • Antigenic characteristics.
  • Geographic association.
  • Vector association.
  • Host association.
  • Disease association.
  • Ecological characteristics.

Species demarcation considers a combination of each of the criteria listed above. While nucleotide sequence relatedness and the resulting phylogenies are important criteria for species demarcation, the other listed criteria may be particularly useful in demarcation of genetically closely related viruses. For example far-eastern (FE) strains of tick-borne encephalitis virus exhibit distinct ecological differences when compared with Omsk haemorrhagic fever virus (OHFV) despite the fact that they are genetically relatively closely related. TBEV-FEs are associated predominantly with Ixodes persulcatus ticks in forest environments in far-east Russia, whereas OHFV is found in the Steppe regions of western Siberia associated particularly with Dermacentor spp. and to a lesser extent with Ixodes spp. These viruses are also antigenically distinguishable in neutralization tests that employ convalescent sera.

Louping ill virus (LIV) and TBEV provide another example where, despite their close genetic relationships and similar host ranges, they display different ecologies (moorlands versus forests), pathogenicities (red grouse, sheep/goats versus humans) and geographical distributions (UK versus Europe/Eurasia), thus justifying their classification as the distinct species, Louping ill virus and Tick-borne encephalitis virus.

On the other hand, the four dengue virus serotypes comprise a single species (Dengue virus), despite being phylogenetically and antigenically quite distinct. This is justified by the fact that they co-circulate in the same geographical areas and ecological habitats, and that they exploit identical vectors, exhibit similar life cycles and disease manifestations.

Member species

SpeciesVirus name(s)Exemplar isolateExemplar accession numberExemplar RefSeq numberAvailable sequenceOther isolatesOther isolate accession numbersVirus abbreviationIsolate abbreviation
Apoi virusApoi virusApMARAF160193NC_003676Complete genomeAPOIV
Aroa virusAroa virus; Bussuquara virusBeAn 4073AY632536NC_009026Complete genomeAROAV
Bagaza virusBagaza virusDakAr B209AY632545NC_012534Complete genomeBAGV
Banzi virusBanzi virusSAH 366DQ859056Complete genomeBANV
Bouboui virusBouboui virusDAK AR B490DQ859057NC_033693Complete genomeBOUV
Bukalasa bat virusBukalasa bat virusUGBP-111AF013365Partial genomeBBV
Cacipacore virusCacipacoré virusBeAn 3276000KF917536NC_026623Complete genomeCPCV
Carey Island virusCarey Island virusP70-1215AF013368Partial genomeCIV
Cowbone Ridge virusCowbone Ridge virusW-10986AF013370Partial genomeCRV
Dakar bat virusDakar bat virus209AF013371Partial genomeDBV
Dengue virusdengue virus2 (16681)U87411NC_001474Complete genomeDENV
Edge Hill virusEdge Hill virusYMP 48DQ859060NC_030289Complete genomeEHV
Entebbe bat virusEntebbe bat virusUgIL-30DQ837641NC_008718Complete genomeENTV
Gadgets Gully virusGadgets Gully virusAusDQ235145NC_033723Complete genomeGGYV
Ilheus virusIlhéus virusOriginalAY632539NC_009028Complete genomeILHV
Israel turkey meningoencephalomyelitis virusIsrael turkey meningoencephalomyelitis virusAF013377Partial genomeITV
Japanese encephalitis virusJapanese encephalitis virusJaOArS982M18370NC_001437Complete genomeJEV
Jugra virusJugra virusP-9-314DQ859066NC_033699Complete genomeJUGV
Jutiapa virusJutiapa virusJG-128KJ469371NC_026620Complete genomeJUTV
Kadam virusKadam virusUgandaDQ235146NC_033724Complete genomeKADV
Kedougou virusKédougou virusDakAar D1470AY632540NC_012533Complete genomeKEDV
Kokobera virusKokobera virusAusMRM 32AY632541NC_009029Complete genomeKOKV
Koutango virusKoutango virusDak Ar D1470AF013384Partial genomeKOUV
Kyasanur Forest disease virusKyasanur Forest disease virusAY323490NC_039218Complete genomeKFDV
Langat virusLangat virusTP21AF253419NC_003690Complete genomeLGTV
Louping ill viruslouping ill virus369/T2Y07863NC_001809Complete genomeLIV
Meaban virusMeaban virusFranceDQ235144NC_033721Complete genomeMEAV
Modoc virusModoc virusM544AJ242984NC_003635Complete genomeMODV
Montana myotis leukoencephalitis virusMontana myotis leukoencephalitis virusUSAAJ299445NC_004119Complete genomeMMLV
Murray Valley encephalitis virusMurray Valley encephalitis virus1-51AF161266NC_000943Complete genomeMVEV
Ntaya virusNtaya virusIPDIAJX236040NC_018705Complete genomeNTAV
Omsk hemorrhagic fever virusOmsk hemorrhagic fever virusBogoluvovskaAY193805NC_005062Complete genomeOHFV
Phnom Penh bat virusPhnom Penh bat virusCAMA-38DAF013394NC_034007Partial genomePPBV
Powassan virusPowassan virusLBL06436NC_003687Complete genomePOWV
Rio Bravo virusRio Bravo virusRiMARAF144692NC_003675Complete genomeRBV
Royal Farm virusRoyal Farm virusAfghanistanDQ235149NC_039219Complete genomeRFV
Saboya virusSaboya virusDak AR D4600DQ859062NC_033697Complete genomeSABV
Saint Louis encephalitis virusSt. Louis encephalitis virusKern217DQ525916NC_007580Complete genomeSLEV
Sal Vieja virusSal Vieja virus38TWM-106AF013401Partial genomeSVV
San Perlita virusSan Perlita virus71V-1251AF013402Partial genomeSPV
Saumarez Reef virusSaumarez Reef virusAustraliaDQ235150NC_033726Complete genomeSREV
Sepik virusSepik virusMK7148DQ837642NC_008719Complete genomeSEPV
Tembusu virusTembusu virusJS804JF895923NC_015843Complete genomeTMUV
Tick-borne encephalitis virustick-borne encephalitis virusNeudoerflU27495NC_001672Complete genomeTBEV
Tyuleniy virusTyuleniy virusLEIV-6CKF815939NC_023424Complete genomeTYUV
Uganda S virusUganda S virusUgandaDQ859065NC_033698Complete genomeUGSV
Usutu virusUsutu virusVienna 2001AY453411NC_006551Complete genomeUSUV
Wesselsbron virusWesselsbron virusSAH177EU707555NC_012735Complete genomeWESSV
West Nile virusWest Nile virus956M12294NC_001563Complete genomeWNV
Yaounde virusYaoundé virusDakAr Y276AF013413NC_034018Partial genomeYAOV
Yellow fever virusyellow fever virus17DX03700NC_002031Complete genomeYFV
Yokose virusYokose virusOita36AB114858NC_005039Complete genomeYOKV
Zika virusZika virusMR766AY632535NC_012532Complete genomeZIKV

Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.
Download GenBank/EMBL query for sequences listed in the table here.

Related, unclassified viruses

Virus name

Accession number

Virus abbreviation

Mammalian tick-borne



Karshi virus






Spondweni virus



Insect-specific flaviviruses



Aedes flavivirus



cell fusing agent virus



Culex flavivirus



Culex theileri flavivirus



Hanko virus



Kamiti River virus



mosquito flavivirus



Nakiwogo virus



Nienokoue virus



Palm creek virus



Quảng Bình virus



Ecuador Paraiso Escondido virus



Viruses with no known arthropod vector



Cháoyáng virus



Lammi virus



Ngoye virus



nounané virus



Tamana bat virus



Virus names and virus abbreviations are not official ICTV designations.
Download GenBank/EMBL query for sequences listed in the table here.