Family: Flaviviridae

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. 

Virion

Morphology

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, which is proteolytically cleaved into M 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. 

dengue virus

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 12.5Å resolution (left) and mature dengue virus at 10Å 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 by exposure to 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 9.2–11.0 kb. 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 terminate with the conserved dinucleotide CU. 

Proteins

Virions contain three structural proteins: capsid (C, 11 kDa), the major envelope protein (E, 50 kDa), , 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 of the genus harbour sequences that appear to 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. 

Lipids

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

Carbohydrates

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). 

Flavivirus genome organization

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 rather than 200S) and exhibits haemagglutination activity. 

Biology

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), while others can infect and replicate in a wide variety of species (mammals, birds, etc.). The usual route of infection for arthropods is 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 unclassified viruses in the genus, including cell fusing agent virus, appear only to infect mosquitoes, and several more, highly genetically distinct insect-only flaviviruses have now been identified (Blitvich and Firth 2015). 

Transmission

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 between 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 transmitted trans-ovarially or vertically (mosquitoes, ticks) and transstadially (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 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). 

Pathogenicity

More than 50% of known flaviviruses have been associated with human disease, including many important human pathogens such as 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. 

Antigenicity

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. 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. The prM and NS1 proteins can also induce antibodies that protect infected animals from lethal infection. 

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 the 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 despite the fact that they are genetically relatively closely related. FE strains of tick-borne encephalitis virus are associated predominantly with Ixodes persulcatus ticks in forest environments in far-east Russia, whereas Omsk hemorrhagic fever virus 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 and tick-borne encephalitis virus provide another example of viruses 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 members of the distinct species, Louping ill virus and Tick-borne encephalitis virus

On the other hand, the four dengue virus serotypes all belong to 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 (Table 1. Flavivirus). 

Table 1.FlavivirusFlaviviruses grouped by vector and host. 

Virus species

Virus name

Accession number

Virus abbreviation

Tick-borne, mammalian host

Gadgets Gully virus

Gadgets Gully virus

DQ235145

GGYV

Kyasanur Forest disease virus

Kyasanur Forest disease virus

AY323490

KFDV

 

Alkhumra hemorrhagic fever virus

AF331718

AHFV

Langat virus

Langat virus

AF253419

LGTV

Louping ill virus

Louping ill virus

Y07863

LIV

 

British subtype

D12937

LIV-Brit

 

Irish subtype

X86784

LIV-Ir

 

Spanish subtype

DQ235152

LIV-Spain

 

Turkish sheep encephalitis virus subtype

DQ235151

TSEV

 

Greek goat encephalitis virus subtype

DQ235153

GGEV

Omsk hemorrhagic fever virus

Omsk hemorrhagic fever virus

AY193805

OHFV

Powassan virus

Powassan virus

L06436

POWV

 

deer tick virus

AF311056

DTV

Royal Farm virus

Royal Farm virus

DQ235149

RFV

Tick-borne encephalitis virus

European subtype

U27495

TBEV-Eur

 

Far Eastern subtype

X07755

TBEV-FE

 

Siberian subtype

L40361

TBEV-Sib

Tick-borne, seabird host

Meaban virus

Meaban virus

DQ235144

MEAV

Saumarez Reef virus

Saumarez Reef virus

DQ235150

SREV

Tyuleniy virus

Tyuleniy virus

KF815939

TYUV

Probably tick-borne

 

 

 

Kadam virus

Kadam virus

DQ235146

KADV

Mosquito-borne, Aroa virus group

Aroa virus

Aroa virus

AY632536

AROAV

 

Bussuquara virus

AF013366

BSQV

 

Iguape virus

AF013375

IGUV

 

Naranjal virus

AF013390

NJLV

Mosquito-borne, Dengue virus group

Dengue virus

Dengue virus 1

U88536

DENV-1

 

Dengue virus 2

U87411

DENV-2

 

Dengue virus 3

M93130

DENV-3

 

Dengue virus 4

AF326573

DENV-4

Mosquito-borne, Japanese encephalitis virus group

Cacipacore virus

Cacipacoré virus

KF917536

CPCV

Japanese encephalitis virus

Japanese encephalitis virus

M18370

JEV

Koutango virus

Koutango virus

AF013384

KOUV

Murray Valley encephalitis virus

Alfuy virus

AF013360

ALFV

 

Murray Valley encephalitis virus

AF161266

MVEV

St Louis encephalitis virus

St. Louis encephalitis virus

DQ525916

SLEV

Usutu virus

Usutu virus

AY453411

USUV

West Nile virus

Kunjin virus

D00246

KUNV

 

West Nile virus

M12294

WNV

Yaounde virus

Yaoundé virus

AF013413

YAOV

Mosquito-borne, Kokobera virus group

Kokobera virus

Kokobera virus

AY632541

KOKV

 

Stratford virus

AF013407

STRV

Mosquito-borne, Ntaya virus group

Bagaza virus

Bagaza virus

AY632545

BAGV

Ilheus virus

Ilhéus virus

AY632539

ILHV

 

Rocio virus

AF013397

ROCV

Israel turkey meningoencephalitis virus

Israel turkey meningoencephalitis virus

AF013377

ITV

Ntaya virus

Ntaya virus

JX236040

NTAV

Tembusu virus

Tembusu virus

JF895923

TMUV

Zika virus

Zika virus

AY632535

ZIKV

Mosquito-borne, yellow fever virus group

Sepik virus

Sepik virus

DQ837642

SEPV

Wesselsbron virus

Wesselsbron virus

EU707555

WESSV

Yellow fever virus

yellow fever virus

X03700

YFV

Probably mosquito-borne, Kedougou virus group 

Kedougou virus

Kédougou virus

AY632540

KEDV

Probably mosquito-borne, Edge Hill virus group 

Banzi virus

Banzi virus

DQ859056

BANV

Bouboui virus

Bouboui virus

DQ859057

BOUV

Edge Hill virus

Edge Hill virus

DQ859060

EHV

Jugra virus

Jugra virus

DQ859066

JUGV

Saboya virus

Potiskum virus

DQ859067

POTV

 

Saboya virus

DQ859062

SABV

Uganda S virus

Uganda S virus

DQ859065

UGSV

Unknown vector, Entebbe bat virus group

Entebbe bat virus

Entebbe bat virus

DQ837641

ENTV

 

Sokuluk virus

AF013405

SOKV

Yokose virus

Yokose virus

AB114858

YOKV

Unknown vector, Modoc virus group

Apoi virus

Apoi virus

AF160193

APOIV

Cowbone Ridge virus

Cowbone Ridge virus

AF013370

CRV

Jutiapa virus

Jutiapa virus

KJ469371

JUTV

Modoc virus

Modoc virus

AJ242984

MODV

Sal Vieja virus

Sal Vieja virus

AF013401

SVV

San Perlita virus

San Perlita virus

AF013402

SPV

Unknown vector, Rio Bravo virus group

Bukalasa bat virus

Bukalasa bat virus

AF013365

BBV

Carey Island virus

Carey Island virus

AF013368

CIV

Dakar bat virus

Dakar bat virus

AF013371

DBV

 Montana myotis leukoencephalitis virus

Montana myotis leukoencephalitis virus

AJ299445

MMLV

Phnom Penh bat virus

Batu Cave virus

AF013369

BCV

 

Phnom Penh bat virus

AF013394

PPBV

Rio Bravo virus

Rio Bravo virus

AF144692

RBV

Member species

The Member Species table enumerating important virus exemplars classified under each species of the genus is provided at the bottom of the page.

 

Related, unclassified viruses

Virus name

Accession number

Virus abbreviation

Mammalian tick-borne

   

Karshi virus

DQ235147

KSIV

Mosquito-borne

   

Fitzroy River virus

KM361634

FRV

Spondweni virus

DQ859064

SPOV

T’Ho virus

EU879061

 

Insect-specific flaviviruses

   

Aedes flavivirus

AB488408

AEFV

Aedes galloisi flavivirus

 

AGFV

Anopheles flavivirus

KX148546

AnFV

Calbertado virus

EU569288

CLBOV

cell fusing agent virus

M91671

CFAV

Cuacua virus

KX245154

CuCuV

Culex flavivirus

GQ165808

CXFV

Culex theileri flavivirus

HE574574

CXthFV

Culiseta flavivirus

KT599442

CsFV

Ecuador Paraiso Escondido virus

KJ152564

EPEV

Hanko virus

JQ268258

HaFV

Kamiti River virus

AY149905

KRV

Mercadeo virus

KP688058

MECDV

mosquito flavivirus

KC464457

MoFV

Nakiwogo virus

GQ165809

NAKV

Nienokoue virus

JQ957875

NiFV

Palm Creek virus

KC505248

PCFV

Parramatta River virus

KT192549

PaRV

Quảng Bình virus

FJ644291

QBV

Xishuangbanna aedes

flavivirus

KU201526

XFV

Yamadai flavivirus

AB981186

YDFV

Viruses with no known arthropod vector

   

Barkedji virus

KC496020

BJV

Cháoyáng virus

FJ883471

CHAOV

Donggang virus

JQ086551

DONV

Ilomantsi virus

KC692067

ILOV

Kampung Karu virus

KY320648

KPKV

Lammi virus

FJ606789

LAMV

La Tina virus

KY320649

LTNV

Long Pine Key virus

KY290256

LPKV

Marisma mosquito virus

MF139576

MMV

Nanay virus

MF139575

NANV

Ngoye virus

DQ400858

NGOV

Nhumirim virus

KJ210048

NHUV

nounané virus

EU159426

NOUV

Tamana bat virus

AF285080

TABV

Segmented flavi-like viruses

   

Jingmen tick virus

KJ001579;
KJ001580;
KJ001581;
KJ001582

JMTV

Mogiana tick virus

JX390986;
KY523073;
JX390985;
KY523074

MGTV

Alongshan virus

MH158415;
MH158416;
MH158417;
MH158418

ASV

Guaico Culex virus

KM461666;
KM461667;
KM461668;
KM461669;
KM461670

GCXV

Shuangao insect virus 7

KR902717;
KR902718;
KR902719;
KR902720

SAIV7

Wuhan flea virus

KR902713;
KR902714;
KR902715;
KR902716

WHFV

Wuhan aphid virus 1

KR902721;
KR902722;
KR902723;
KR902724

WHAV1

Wuhan aphid virus 2

KR902725;
KR902726;
KR902727;
KR902728

WHAV2

Wuhan cricket virus

KR902709;
KR902710;
KR902711;
KR902712

WHCV

Virus names and virus abbreviations are not official ICTV designations.