Part II – The Positive Sense Single Stranded RNA Viruses

Family Betaflexiviridae
Taxonomic structure of the family
Family Betaflexiviridae
Genus   Capillovirus
Genus   Carlavirus
Genus   Citrivirus
Genus   Foveavirus
Genus   Trichovirus
Genus   Vitivirus

Distinguishing features
The family contains viruses infecting plants which share a distinct lineage of alphavirus-like repli-
cation proteins.

Virion properties
Morphology
Virions are flexuous filaments, usually 12–13 nm in diameter (range 10–15 nm) and from 600 to
over 1000 nm in length, depending on the genus. They have helical symmetry with a pitch of about
3.4 nm (range 3.3–3.7 nm) and in some genera there is clearly visible cross-banding.
Physicochemical and physical properties
Virions sediment as single (or occasionally two very close) bands with an S20,w of 92–176S, depend-
ing on the genus.
Nucleic acid
Virions contain a single molecule of linear ssRNA of about 5.9–9.0 kb which is 5–6% by weight of
the virion. The RNA is capped (or probably capped) at the 5’ terminus with m7G and has a poly­
adenylated tract at the 3’ terminus. In the genus Carlavirus some viruses have two subgenomic
RNAs (sgRNAs) of 2.1–3.3 kb and 1.3–1.6 kb, which are possibly encapsidated in shorter particles.
Proteins
The viral capsid of all members is composed of a single polypeptide ranging in size from 18 to
44 kDa.
Lipids
None reported.
Carbohydrates
None reported.

Genome organization and replication

The number of genes is between three and six depending upon the genus (Figure 1) but, in all
species, the ORF1-encoded product, which follows a short 5’-UTR sequence, has homologies
with polymerase proteins of the “alphavirus-like” supergroup of RNA viruses. This protein (190–
250 kDa) contains the conserved domains for methyltransferase (Mtr), helicase (Hel) and RNA-
dependent RNA polymerase (RdRp) activity. Most members also have AlkB and papain-like
protease (P-Pro) domains between the Mtr and Hel. Smaller ORFs encode the proteins involved
in cell-to-cell movement, either a single MP of the “30K” superfamily (Capillovirus, Citrivirus,
Trichovirus, Vitivirus) or a “triple gene block” (TGB) (remaining genera and viruses). These are usu-
ally located following (3’-proximal to) the polymerase but in capillovirus genomes the MP ORF2 is
nested within the ORF1 and in vitiviruses an extra ORF is present between the polymerase and MP
genes. The CP gene always follows the MP(s) and in some genera (Carlavirus, Vitivirus and some
trichoviruses) a final ORF encodes a protein with a zinc binding finger motif and the ability to bind
nucleic acids. In vitiviruses, this small protein has been shown to have RNA silencing suppressor

Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses

920 © 2012 International Committee on Taxonomy of Viruses. Published by Elsevier Inc. All Rights Reserved.
 Betaflexiviridae

activity. ORFs downstream of the polymerase are translated from 3’-terminal sgRNAs that can
often be found in infected tissue. In some viruses, notably in the genera Citrivirus, Vitivirus and
Trichovirus, nested sets of 5’-terminal sgRNAs and their associated dsRNAs can also be detected.
Replication is (or is presumed to be) cytoplasmic and the product of ORF1 is the only virus-encoded
protein known to be involved.

Antigenic properties
Virions are highly immunogenic in members of the genus Carlavirus but those of other genera are
only moderate to poor antigens. Within (but not usually between) genera, some viruses are sero-
logically related.

Biological properties
Members have been reported from a diverse range of plant species but the host range of individual
members is usually limited. With the exception of most members of the genus Carlavirus, natural
infections are mostly or exclusively of woody hosts. Many of the viruses have relatively mild effects
on their host. All species can be transmitted by mechanical inoculation, although some with dif-
ficulty. Many of the viruses have no known invertebrate or fungus vectors; however some tricho-
viruses are known to be mite-borne, most carlaviruses are transmitted naturally by aphids in the
non-persistent manner and a range of vectors (pseudococcid mealybugs, scale insects and aphids)
have been reported for different vitiviruses. Aggregates of virus particles accumulate in the cyto-
plasm. Many carlaviruses induce the formation of ovoid or irregularly shaped inclusions but other-
wise there are usually no specific cytopathic structures.

Table 1:  Distinguishing properties of genera in the family Betaflexiviridae

Genus Virion length ORFs Repa MP(s)b CPc

(nm)
Capillovirus 640–700 2 210–245 30K 25–27
Carlavirus 610–700 6 215–225 TGB 32–36
Citrivirus 960 3 227 30K 41
Foveavirus 800  5 230–250 TGB 28–44
Trichovirus 640–890 3 or 4 215–220 30K 21–24

Pos. ssRNA
Vitivirus 725–785 5 190–200 30K 18–22
a
Rep, Replication protein size (kDa).
b
MP, Movement protein either of the “30K” superfamily or a triple gene block (TGB).
c
CP, Coat protein size (kDa).

Figure 1:  (Left) Schematic representation of a fragment of a particle of a capillovirus. (Right) Negative contrast
electron micrograph of particles of an isolate of the species Apple stem grooving virus. The bar represents 100 nm.
(Courtesy of N. Yoshikawa.)

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Part II – The Positive Sense Single Stranded RNA Viruses

Species and genus demarcation criteria in the family

Genera are distinguished by various features of genome organization and the natural mode of trans-
mission. These are summarized in Table 1. Throughout the family, isolates of different species should
have less than about 72% nt identity (or 80% aa identity) between their respective CP or polymerase
genes. Viruses from different genera usually have less than about 45% nt identity in these genes.

Genus Capillovirus
Type species Apple stem grooving virus
Distinguishing features
Capilloviruses have a distinctive genomic organization, with two ORFs encoding a large replica-
tion-associated protein fused with the coat protein and (as a nested ORF) a putative movement pro-
tein. The MP and CP are expressed from subgenomic RNAs. No vectors are known. Virions have
prominent cross-banding.

Virion properties
Morphology
Virions are flexuous filaments, 640–700  12 nm, constructed from helically arranged protein sub­
units in a primary helix with a pitch of 3.4 nm and between 9 and 10 subunits per turn with promi-
nent cross-banding (see Figure 1 above).
Physicochemical and physical properties
The S20,w of particles is about 112S, isoelectric point is about pH 4.3 at ionic strength 0.1 M, and
electrophoretic mobility is 10.3 and 6.5 105 cm2 sec1 volt1, at pH 7.0 and 6.0 respectively (ionic
strength 0.1 M; data for apple stem grooving virus).
Nucleic acid
Virions contain linear positive sense ssRNA, 6.5–7.4 kb in size, constituting about 5%, by weight,
of virions. The RNA is polyadenylated at its 3’ end. Isolates of the species Apple stem grooving virus
from different hosts show wide variations in the sequence of a 284 aa region of ORF1-encoded pro-
tein, between the polymerase and CP domains.
Proteins
Virions are composed of a single 24–27 kDa protein.

Genome organization and replication

The genomic RNA of all sequenced viruses has the same organization, and two ORFs (Figure 2). ORF1
encodes a 240–266 kDa protein followed by a UTR of 140–300 nt upstream of the 3’-poly(A) tail. ORF2
is nested within ORF1 near its 3’ end, and encodes a 36–52 kDa protein. Although the CP cistron is
located in the C-terminal end of ORF1, and ORF2 is nested within ORF1, the strategy of expression

Apple stem grooving virus, ASGV (6,495 nts)

ORF1 ORF3
Mtr P-Pro Hel RdRp CP
5′m G
7 A(n) 3′OH
MP
ORF2

Figure 2:  Genome organization of apple stem grooving virus showing the relative positions of the ORFs and
their expression products. Mtr, methyltransferase; P-Pro, papain-like protease; Hel, helicase; RdRp, RNA-
dependent RNA polymerase; MP, putative movement protein; CP, capsid protein.

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 Betaflexiviridae

of both CP and putative MP may be based on sgRNA production, as suggested by the analysis of
dsRNA patterns from infected tissues. dsRNAs of the type member consist of five major bands with
sizes of approximately 6.5, 5.5, 4.5, 2.0 and 1.0 kbp. The 6.5 kbp species probably represents the dou-
ble stranded form of the full-length genome, and the 2.0 and the 1.0 kbp species may be the double-
stranded forms of sgRNAs that code for the putative MP and the CP, respectively. Replication is likely
to occur in the cytoplasm, in which virus particles accumulate in discrete bundles.

Antigenic properties
Virions are moderately antigenic. There are no serological relationships between species.

Biological properties
Host range
Apple stem grooving virus (ASGV) is pathogenic to pome fruits and citrus and induces stock/scion
incompatibility, i.e. top-working disease of apple and bud union crease syndrome of citrus. It also
infects lily. Cherry virus A (CVA) is frequently found in sweet and sour cherry (and less frequently
in other Prunus hosts) but no disease has been associated with it.
Transmission
No vectors are known. ASGV was transmitted through seed to progeny seedlings of Chenopodium
quinoa, and lily. ASGV, CVA, and Nandina stem pitting virus (NSPV) are transmitted by grafting.
NSPV has not been transmitted by sap inoculation, but by slashing stems with a partially purified
virus preparation.
Geographical distribution
Geographical distribution ranges from wide to restricted according to the virus. ASGV has been
recorded from most areas where apples are grown, and is widespread in citrus in China, Japan,
United States, Australia and South Africa. CVA is widespread and probably occurs worldwide in
cherry hosts. NSPV is found only in the United States.
Cytopathic effects
No distinct cytological alterations have been observed in infected cells. Virus particles occur in
bundles in mesophyll and phloem parenchyma cells, but not in the epidermis and sieve elements.

Species demarcation criteria in the genus

The criteria demarcating species in the genus are:

Pos. ssRNA
l Natural host range.
l Serological specificity (all known species are serologically unrelated).
l Less than about 72% nt identity (or 80% aa identity) between their CP or polymerase genes.

List of species in the genus Capillovirus

Apple stem grooving virus
  Apple stem grooving virus-P-209 [D14995  NC_001749] (ASGV-P209)
Citrus tatter leaf virus-lily [D16681] (CTLV-L)
Cherry virus A
  Cherry virus A-Germany [X82547  NC_003689] (CVA-DE)
Species names are in italic script; names of isolates and strains are in roman script. Sequence accessions [ ] and assigned
abbreviations ( ) are also listed.

List of other related viruses which may be members of the genus Capillovirus but have not
been approved as species
Nandina stem pitting virus (NSPV)

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Part II – The Positive Sense Single Stranded RNA Viruses

Genus Carlavirus
Type species Carnation latent virus
Distinguishing features
Carlaviruses have six ORFs, including a TGB, and are insect-transmitted.

Virion properties
Morphology
Virions are slightly flexuous filaments, 610–700 nm in length and 12–15 nm in diameter (Figure 3).
They have helical symmetry with a pitch of about 3.4 nm.
Physicochemical and physical properties
Virion Mr is about 60 106, with a nucleic acid content of about 6%. Virion S20,w is 147–176S, and the
buoyant density in CsCl solutions is 1.3 g cm3.
Nucleic acid
Virions contain a single molecule of linear ssRNA that has a size range of 7.4–7.7 kb when estimated
by agarose gel analysis, although full-length sequence analysis suggests that genome sizes are in the
8.3–8.7 kb range. Some species also have two sgRNAs of 2.1–3.3 kb and 1.3–1.6 kb, which are possi-
bly encapsidated in shorter particles. The genomic RNAs have a 3’-poly(A) tract and a 5’-cap.

Genome organization and replication

There are typically six ORFs with short UTRs at the 5’ and 3’ termini. In potato virus M (Figure 4),
ORF1 encodes a polypeptide of 223 kDa that is the viral replicase; ORFs 2, 3 and 4 form the triple
gene block and encode polypeptides of 25, 12 and 7 kDa which facilitate virus movement. ORF5
encodes the 34 kDa CP and overlaps ORF6, which encodes a cysteine-rich protein of 11–16 kDa. The
function of the 11–16 kDa polypeptide has yet to be determined, but its ability to bind nucleic acid
indicates that it may facilitate aphid transmission or be involved in host gene transcription/gene
silencing and/or viral RNA replication.

Figure 3:  Filamentous particles of an isolate of the species Carnation latent virus. The bar represents 100 nm.
(Courtesy R.G. Milne.)

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 Betaflexiviridae

Potato virus M, PVM (8,533 nts) TGB

25K 7K 11K
223K NB
5′m G
7 A(n) 3′OH
Mtr AlkB P-Pro Hel RdRp CP
12K 34K

Figure 4:  Genome organization of potato virus M showing the relative positions of the ORFs and their expres-
sion products. Mtr, methyltransferase; P-Pro, papain-like protease; Hel, helicase; RdRp, RNA-dependent RNA
polymerase; CP, capsid protein; NB, nucleic acid binding protein. The 25K, 12K and 7K proteins constitute the
triple gene block.

Only ORF1 is translated from the full length genomic RNA. With blueberry scorch virus and prob-
ably other carlaviruses the product of ORF1 is proteolytically processed by a papain-like proteinase
activity, with about 30–40 kDa being removed. The 3’-terminal ORFs appear to be translated from
two sgRNAs that can be found in infected tissue, and, for some viruses, can be detected in purified
virus preparations. The 5’-untranslated leader sequence of the genomic RNA and the sgRNA for the
CP of potato virus S (PVS) have both been shown to act as efficient enhancers of translation.

Antigenic properties
Carlavirus virions are good immunogens. Some species are serologically interrelated, but others are
apparently distinct.

Biological properties
Host range
Individual viruses have restricted natural host ranges, but some can infect a wide range of experi-
mental hosts.
Transmission
Most species are transmitted naturally by aphids in the non-persistent manner; cowpea mild mottle
virus (CPMMV) is transmitted by whiteflies (Bemisia tabaci), pea streak virus, red clover vein mosaic
virus and CPMMV are seedborne in their leguminous hosts. All are mechanically transmissible;
some (e.g. carnation latent virus and PVS) are sufficiently infectious to be so transmitted this way in
the field.
Geographical distribution

Pos. ssRNA
The geographical distribution of many species is restricted, but those infecting vegetatively-propa-
gated crops are usually widely distributed, presumably due to inadvertent dissemination in vegeta-
tive propagules. Most species commonly occur in temperate climates, but CPMMV is restricted to
tropical and sub-tropical regions.
Cytopathic effects
Virions of aphid-borne species are scattered throughout the cytoplasm or occur in membrane-
associated bundle-like or plate-like aggregates. Many species also induce the formation of ovoid or
irregularly shaped inclusions that appear in the light microscope as vacuolate bodies; these consist
of aggregates of virus particles, mitochondria, endoplasmic reticulum and lipid globules. The parti-
cles of CPMMV, the whitefly-transmitted carlavirus, also occur in aggregates in cytoplasm; those of
most, but not all, strains of CPMMV form brush-like inclusions.

Species demarcation criteria in the genus

Each distinct species usually has a specific natural host range. Distinct species do not cross-protect
in infected common host plant species. Distinct species are readily differentiated by serological pro-
cedures; strains of individual species are often distinguishable in reactions with polyclonal antisera,
but more readily so with monoclonal antibodies. Distinct species have less than about 72% nt iden-
tity (or 80% aa identity) between their CP or polymerase genes.

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Part II – The Positive Sense Single Stranded RNA Viruses

List of species in the genus Carlavirus

Aconitum latent virus
  Aconitum latent virus-Japan:D [AB051848  NC_002795] (AcLV-D)
American hop latent virus
  American hop latent virus-USA:Washington (AHLV-WA)
State
Blueberry scorch virus
  Blueberry scorch virus-NJ-2 [L25658  NC_003499] (BlScV-nj2)
Cactus virus 2
  Cactus virus 2-Germany (CV-2-DE)
Caper latent virus
  Caper latent virus-Italy (CapLV-IT)
Carnation latent virus
  Carnation latent virus-United Kingdom [AJ010697*] (CLV-UK)
Chrysanthemum virus B
  Chrysanthemum virus B-Japan:Showa [AB245142] (CVB-S)
Cole latent virus
  Cole latent virus-Brazil [AY340584*] (CoLV-BR)
Coleus vein necrosis virus
  Coleus vein necrosis virus-USA [EF527260  NC_009764] (CVNV-USA)
Cowpea mild mottle virus
  Cowpea mild mottle virus-M [AF024629*] (CPMMV-M)
Dandelion latent virus
  Dandelion latent virus-Canada:British Colombia (DaLV-BC)
Daphne virus S
  Daphne virus S-type strain: K [AJ620300  NC_008020] (DVS-K)
Elderberry symptomless virus
  Elderberry symptomless virus-United Kingdom (ElSLV-UK)
Garlic common latent virus
  Garlic common latent virus-Germany [AB004805*] (GarCLV-DE)
Helenium virus S
  Helenium virus S-Germany [D10454*] (HVS-DE)
Helleborus net necrosis virus
  Helleborus net necrosis virus-G5 [FJ196835  NC_012038] (HNNV-G5)
Honeysuckle latent virus
  Honeysuckle latent virus-United Kingdom (HnLV-UK)
Hop latent virus
  Hop latent virus-Japan [AB032469  NC_002552] (HpLV-JA)
Hop mosaic virus
  Hop mosaic virus-Australia [EU527979  NC_010538] (HpMV-AUS)
Hydrangea latent virus
  Hydrangea latent virus-USA (HdLV-USA)
Kalanchoë latent virus
  Kalanchoë latent virus-PV-0290B [FJ531634  NC_013006] (KLV-PV0290B)
Ligustrum necrotic ringspot virus
  Ligustrum necrotic ringspot virus-USA [EU074853  NC_010305] (LNRSV-USA)
Lilac mottle virus
  Lilac mottle virus-USA (LiMoV-USA)
Lily symptomless virus
  Lily symptomless virus-South Korea [AJ516059  NC_005138] (LSV-Kor)
Melon yellowing-associated virus
  Melon yellowing-associated virus-Bessa [AB510477*] (MYaV-Bessa)
Mulberry latent virus
  Mulberry latent virus-Japan (MLV-JP)
Muskmelon vein necrosis virus
  Muskmelon vein necrosis virus-USA:California (MuVNV-CAL)
Narcissus common latent virus
  Narcissus common latent virus-Zhangzhou [AM158439  NC_008266] (NCLV-ZZ)
Narcissus symptomless virus
  Narcissus symptomless virus-Hangzhou [AM182569  NC_008552] (NSV-HZ)
Nerine latent virus
(Hippeastrum latent virus)
  Nerine latent virus-Taiwan [DQ098905  NC_011540] (NeLV-TW)

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 Betaflexiviridae

Passiflora latent virus

  Passiflora latent virus-Israel [DQ455582  NC_008292] (PLV-IS)
Pea streak virus
  Pea streak virus-ATCCPV-87 [AF354652*] (PeSV-ATCCPV87)
Poplar mosaic virus
  Poplar mosaic virus-PV-0341 [AY505475  NC_005343] (PopMV-PV0341)
Potato latent virus
  Potato latent virus-Canada [EU433397  NC_011525] (PotLV-CAN)
Potato virus M
  Potato virus M-Russian wild type [D14449  NC_001361] (PVM-RU)
Potato virus P
  Potato virus P-Brazil [EU338239] (PVP-BRZ)
  Potato rough dwarf virus [EU020009  NC_009759] (PRDV)
Potato virus S
  Potato virus S-Leona [AJ863509  NC_007289] (PVS-Leona)
Red clover vein mosaic virus
  Red clover vein mosaic virus-Washington [FJ685618  NC_012210] (RCVMV-Washington)
Shallot latent virus
  Shallot latent virus-YH1 [AJ292226  NC_003557] (SLV-YH1)
Sint-Jan’s onion latent virus
  Sint-Jan’s onion latent virus-Netherlands (SJOLV-NL)
Strawberry pseudo mild yellow edge virus
  Strawberry pseudo mild yellow edge virus-USA (SPMYEV-USA)
Sweet potato chlorotic fleck virus
  Sweet potato chlorotic fleck virus-Uganda [AY461421  NC_006550] (SPCFV-UG)
Verbena latent virus
  Verbena latent virus-Israel [AF271218*] (VeLV-IS)
Species names are in italic script; names of isolates are in roman script; names of synonyms are in roman script and
parentheses. Sequence accession numbers [ ] and assigned abbreviations ( ) are also listed.
*Sequences do not comprise the complete genome.

List of other related viruses which may be members of the genus Carlavirus but have not
been approved as species
Arracacha latent virus (ALV)
Artichoke latent virus M (ArLVM)
Artichoke latent virus S (ArLVS)
Butterbur mosaic virus [AB517596   NC_013527] (ButMV)
Cardamine latent virus (CaLV)

Pos. ssRNA
Carrot virus S [EU881919*] (CarVS)
Helleborus mosaic virus [FJ196838*] (HeMV)
Hydrangea chlorotic mottle virus [EU754720   NC_012869] (HCMoV)
Phlox virus B [EU162589   NC_009991] (PhlVB)
Phlox virus M [EF507476*] (PhlVM)
Phlox virus S [EF492068   NC_009383] (PhlVS)
Sedum latent virus [FJ560901*] (SeLV)
*Sequences do not comprise the complete genome.

Genus Citrivirus
Type species Citrus leaf blotch virus
Distinguishing features
This genus consists of a single species. There are three ORFs, similar to trichoviruses, but it is dis-
tinct from them in phylogenetic analyses, has longer virions and a much larger coat protein that
more closely resembles those of foveaviruses.

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Part II – The Positive Sense Single Stranded RNA Viruses

Virion properties
Morphology
Virions are slightly flexuous filaments, 960 nm in length and 12–15 nm in diameter (Figure 5).
Physicochemical and physical properties
No information.
Nucleic acid
Virions contain a single molecule of positive sense ssRNA, about 8.7 kb long. There is a methylated
cap at the 5’ terminus and a polyadenylated 3’ terminus.
Proteins
The viral capsid is composed of a single polypeptide of about 41 kDa.

Genome organization and replication

The genome contains three ORFs (Figure 6). ORFs 2 and 3 are separated by a short intergenic region
and ORFs 1 and 2 overlap by 1 nt. ORF1 is the replication protein and is probably directly expressed
from genomic RNA. It is assumed that the two smaller downstream ORFs, which code respectively
for the putative “30K” MP and CP, are expressed via sgRNAs.

Antigenic properties
No information.

Biological properties
Host range
The virus causes abnormal bud union and leaf blotching in various citrus varieties. Citrus is the
only known natural host and mechanical transmission to a range of herbaceous hosts has been
unsuccessful.

Figure 5:  Negative contrast electron micrograph of particles of an isolate of the species Citrus leaf blotch virus.
The bar represents 200 nm.

Citrus leaf blotch virus, CLBV (8,747nts)

ORF1 ORF3
Mtr AlkB P-Pro Hel RdRp CP
5′m7G A(n) 3′OH
MP
ORF2

Figure 6:  Genome organization of citrus leaf blotch virus showing the relative positions of the ORFs and their
expression products. Mtr, methyltransferase; P-Pro, papain-like protease; Hel, helicase; RdRp, RNA-dependent
RNA polymerase; MP, putative movement protein; CP, capsid protein.

928
 Betaflexiviridae

Transmission
The virus is transmitted to citrus by grafting. There is no known natural vector.
Geographical distribution
The virus has been reported from citrus germplasm worldwide.
Cytopathic effects
No information.

Species demarcation criteria in the genus

Not applicable.

List of species in the genus Citrivirus

Citrus leaf blotch virus
(Dweet mottle virus)
Citrus leaf blotch virus-SRA-153 [AJ318061  NC_003877] (CLBV-SRA153)
Species names are in italic script; names of isolates are in roman script; names of synonyms are in roman script and
parentheses. Sequence accession numbers [ ] and assigned abbreviations ( ) are also listed.

List of other related viruses which may be members of the genus Citrivirus but have not
been approved as species
None reported.

Genus Foveavirus
Type species Apple stem pitting virus
Distinguishing features
Foveaviruses are distinct in having five ORFs and larger CPs than most other members of the
family.

Pos. ssRNA
Virion properties
Morphology
Virions are flexuous filaments, about 800 to over 1000 nm in length and 12–15 nm in diameter with
helical symmetry exhibiting a surface pattern with cross-banding and longitudinal lines (Figure 7).
Particles of some viruses, including apple stem pitting virus (ASPV), show a tendency for end-to-
end aggregation.
Physicochemical and physical properties
ASPV virions sediment as two or three bands in sucrose density gradients but yield a single band at
equilibrium in Omnipaque 350 density gradients. They resist moderately high temperatures (ther-
mal inactivation is around 60 °C) but not organic solvents, and are unstable in cesium chloride and
sulfate.
Nucleic acid
Virions contain a single molecule of positive sense ssRNA, polyadenylated at the 3’ terminus.
Proteins
The viral capsid of all species is composed of a single polypeptide with a size ranging from 28 kDa
(grapevine rupestris stem pitting-associated virus, GRSPaV) to 44 kDa (ASPV and apricot latent
virus, ApLV).

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Part II – The Positive Sense Single Stranded RNA Viruses

Figure 7:  Negative contrast electron micrograph of particles of an isolate of the species Apple stem pitting virus.
The bar represents 100 nm. (Courtesy of H. Koganezawa.)

Apple stem pitting virus, ASPV (9,306 nts)

TGB
ORF1 25K 7K
Mtr AlkB P-Pro Hel RdRp
5′m7G A(n) 3′OH
247K CP
13K 44K

Figure 8:  Genome organization of apple stem pitting virus showing the relative position of the ORFs and their
expression products. Mtr, methytransferase; P-Pro, papain-like protease; Hel, helicase; Pol, polymerase; TGB,
triple gene block; CP, capsid protein.

Genome organization and replication

The genomes of all fully sequenced members contain five ORFs (Figure 8). The 5’ region initiates
with a UTR of 33–72 nt, ORF1 codes for the replication-related protein, ORF2, ORF3 and ORF4
constitute the TGB and ORF5 is the CP cistron. A non-coding sequence of 176–312 nt followed by
a poly(A) tail terminate the genome. ASPV virions accumulate in the cytoplasm, where multiplica-
tion is likely to occur following a strategy comparable to that of other viruses in the family, based
on direct expression of the 5’-proximal ORF, and expression of downstream ORFs from sgRNAs.
Multiple dsRNAs are found in infected hosts.

Antigenic properties
Antisera to ASPV that can be used for serological detection tests have been raised from purified vir-
ions or chimeric fusion CPs expressed in E. coli. ASPV and ApLV are serologically related, but there
are no recognized serological relationships among other members of the genus.

Biological properties
Host range
The natural host range of individual species is restricted to a single (GRSPaV) or a few hosts (ASPV,
ApLV). ASPV infects primarily pome fruits, causing diseases of apple (topworking disease) when

930
 Betaflexiviridae

grafted on susceptible rootstocks, of pear (vein yellows and necrotic spot) and quince. ApLV is the
putative agent of peach asteroid spot and peach sooty ringspot diseases. GRSPaV is a pathogen of
grapevine. Experimental host ranges are also restricted.
Transmission
No vector is known for any of the viruses. ASPV is transmitted by grafting and persists in the host
propagative material. ASPV is mechanically transmissible, with some difficulty, to Nicotiana occiden-
talis and its subspecies obliqua.
Geographical distribution
All members have a wide geographical distribution.
Cytopathic effects
ASPV elicits a severe derangement of the cytology of infected cells but no specific cytopathic struc-
tures or inclusion bodies. Virus particles accumulate in bundles in the cytoplasm.

Species demarcation criteria in the genus

The criteria demarcating species in the genus are:
l Natural host range.
l Serological specificity.
l CP size.
l Less than about 72% nt identity (or 80% aa identity) between their CP or polymerase genes.

List of species in the genus Foveavirus

Apple stem pitting virus
  Apple stem pitting virus-PA66 [D21829  NC_003462] (ASPV-PA66)
Apricot latent virus
  Apricot latent virus-Caserta12 [AF318062*] (ApLV-Caserta12)
Grapevine rupestris stem pitting-associated virus
  Grapevine rupestris stem pitting-associated [AF057136  NC_001948] (GRSPaV-USA )
virus-USA
Peach chlorotic mottle virus
  Peach chlorotic mottle virus-Agua-4N6 [EF693898  NC_009892] (PCMoV-Agua4N6 )
Species names are in italic script; names of isolates are in roman script. Sequence accession numbers [ ] and assigned
abbreviations ( ) are also listed.
*Sequences do not comprise the complete genome.

Pos. ssRNA
List of other related viruses which may be members of the genus Foveavirus but have not
been approved as species
Asian prunus virus 1 [FJ824737] (APV1)
Asian prunus virus 2 [DQ205237*] (APV2)
Asian prunus virus 3 [DQ205238*] (APV3)
*Sequences do not comprise the complete genome.

Genus Trichovirus
Type species Apple chlorotic leaf spot virus

Distinguishing features
Trichoviruses have three (or sometimes four) ORFs including a movement protein of the “30K”
superfamily.

931
Part II – The Positive Sense Single Stranded RNA Viruses

Figure 9:  Negative contrast electron micrograph of particles of an isolate of the species Apple chlorotic leaf spot
virus. The bar represents 100 nm. (Courtesy of M.A. Castellano.)

Virion properties
Morphology
Virions are very flexuous filaments, 640–890  10–12 nm in size, helically constructed with a pitch of
3.3–3.5 nm, and about 10 subunits per turn of the helix. Virions may show cross banding, criss-cross
or rope-like features according to the negative contrast material used (Figure 9).
Physicochemical and physical properties
Virions sediment as single or as two very close bands with an S20,w of about 100S. Apple chlorotic
leaf spot virus (ACLSV) virions are sensitive to ribonucleases. Virions of all viruses in the genus
resist moderately high temperatures (thermal inactivation is around 55–60 °C) and are moderately
resistant to organic solvents.
Nucleic acid
Virions contain a single molecule of linear, positive sense, ssRNA about 7.5– 8.0 kb in size, with a
polyadenylated 3’ terminus, accounting for about 5% of the particle weight. Indirect evidence sug-
gests that the genome RNA of ACLSV is capped at its 5’-end with m7G. An infectious cDNA clone
of ACLSV has been produced. ACLSV isolates show a high variability in their nt sequence with
an overall identity between 76 and 82%. The CP is the most conserved protein (87–93% identity),
whilst the putative MP is the most divergent (77–85% identity).
Proteins
Virions of all members are composed of a single 20.5–27 kDa polypeptide.

Genome organization and replication

The genomes of ACLSV and grapevine berry inner necrosis virus (GINV) contain three slightly
overlapping ORFs while other members and possible members of the genus have an additional ORF
at the 3’ terminus (Figure 10). The large 5’ ORF of ACLSV is directly expressed from genomic RNA,
whereas the two smaller downstream ORFs that code, respectively, for the MP and CP, are expressed
via sgRNAs. The fourth ORF (where present) has homologies to the vitivirus nucleic acid binding
proteins. ACLSV-infected tissues contain six dsRNA species of approximately 7.5, 6.4, 5.4, 2.2, 1.1
and 1.0 kbp. The 7.5 kbp species represents the double-stranded form of the full-length genome,
whereas the 2.2 and the 1.1 kbp species are the double-stranded forms of sgRNAs coding for the MP
and the CP, respectively. The most abundant dsRNA species, the function of which are unknown,
are 5’ co-terminal with genomic RNA, and have sizes of 6.4 and 5.4 kbp, respectively. Replication is

932
 Betaflexiviridae

Apple chlorotic leaf spot virus, ACLSV (7,555 nts)

ORF1 ORF3
Mtr AlkB P-Pro Hel RdRp CP
5′m G
7
A(n) 3′OH
MP
ORF2
Cherry mottle leaf virus, CMLV (8,018 nts)
ORF1 ORF3 ORF4
Mtr AlkB P-Pro Hel RdRp CP NB
5′m7G A(n) 3′OH
MP
ORF2

Figure 10:  Genome organization of apple chlorotic leaf spot virus and cherry mottle leaf virus, showing the
relative positions of the ORFs and their expression products. Mtr, methyltransferase; P-Pro, papain-like pro-
tease; Hel, helicase; Pol, polymerase; MP, putative movement protein; CP, capsid protein; NB, nucleic acid
binding protein.

presumed to be cytoplasmic and to involve the translation product of ORF1. The MP of ACLSV is a
suppressor of silencing that interferes with systemic movement of the silencing signal.

Antigenic properties
Virions are moderate to poor antigens. Cherry mottle leaf virus (CMLV) and peach mosaic virus
(PcMV) are serologically related to one another but not to the other members of the genus.

Biological properties
Host range
The natural host range of individual species is relatively narrow (ACLSV, PcMV), or restricted to a
single host (GINV, CMLV). The experimental host range is somewhat wider, but still limited to a few
herbaceous species. In the natural hosts, infections induce few or no symptoms (ACLSV in certain
hosts), or mottling, rings, line patterns and fruit injuries (i.e. pseudosharka) (ACLSV), mottling with
stunting and internal necrosis of shoots and berries (GINV), mottling and severe distortion of the
leaves (CMLV), mottling and deformation of leaves and fruits and color break in the petals (PcMV).
Transmission
The viruses are readily transmitted by mechanical inoculation, by grafting (ACLSV, GINV, CMLV,
PcMV) and through propagating material. GINV is transmitted by the grape erineum mite
Colomerus vitis, CMLV by the scale mite Eriophyes inequalis, and PcMV by the peach bud mite

Pos. ssRNA
Eriophyes insidiosus.
Geographical distribution
Geographical distribution varies from wide to restricted, according to the virus. ACLSV is ubiqui-
tous, whereas GINV is reported only from Japan, and CMLV and PcMV from North America.
Cytopathic effects
Infected cells are damaged by ACLSV to varying extents. Virions are found in phloem and par­
enchyma cells of leaves and roots and accumulate in the cytoplasm, sometimes in the nucleus, in
bundles or paracrystalline aggregates. No inclusion bodies are formed.

Species demarcation criteria in the genus

The criteria demarcating species in the genus are:

l Natural and experimental host range.

l Serological specificity.
l Less than about 72% nt identity (or 80% aa identity) between their CP or polymerase genes.
l Transmission by a vector.
l Vector specificity.

933
Part II – The Positive Sense Single Stranded RNA Viruses

List of species in the genus Trichovirus

Apple chlorotic leaf spot virus
  Apple chlorotic leaf spot virus-P863 [M58152  NC_001409] (ACLSV-P863)
Apricot pseudo-chlorotic leaf spot virus
  Apricot pseudo-chlorotic leaf spot virus-Sus2 [AY713379  NC_006946] (APsCLSV-Sus2)
Cherry mottle leaf virus
  Cherry mottle leaf virus-SA1162-21 [AF170028  NC_002500] (CMLV-SA116221)
Grapevine berry inner necrosis virus
  Grapevine berry inner necrosis virus-Japan [D88448  NC_015220] (GINV-JP)
Peach mosaic virus
  Peach mosaic virus-2022-01 (CA-1) [DQ117579  NC_011552] (PcMV-202201 (CA1))
Species names are in italic script; names of isolates are in roman script. Sequence accession numbers [ ] and assigned
abbreviations ( ) are also listed.

List of other related viruses which may be members of the genus Trichovirus but have not
been approved as species
Fig latent virus 1 [FN377573*] (FLV-1)
Phlomis mottle virus [AM920542*] (PhMV)
*Sequences do not comprise the complete genome.

Genus Vitivirus
Type species Grapevine virus A
Distinguishing features
Vitiviruses have a distinctive genome organization with five ORFs, including a 20K ORF between
the polymerase and the movement protein of the “30K” superfamily. Natural transmission is by
pseudococcid mealybugs, soft scale insects and aphids.

Virion properties
Morphology
Virions are flexuous filaments 725–825  12 nm in size, showing distinct cross-banding, helically
constructed with a pitch of 3.3–3.5 nm and about 10 subunits per turn of the helix (Figure 11).

Figure 11:  Negative contrast electron micrograph of particles of an isolate of the species Grapevine virus A. The
bar represents 100 nm. (Courtesy of A.A. Castellano.)

934
 Betaflexiviridae

Physicochemical and physical properties

Virions sediment as a single or two very close bands in sucrose or Cs2SO4 gradients, with an S20,w
of about 92S. Virions of Heracleum latent virus (HLV) are sensitive to ribonucleases. Virions of all
members of the genus resist moderately high temperatures (thermal inactivation is around 60 °C)
and are moderately resistant to organic solvents.
Nucleic acid
Virions contain a single molecule of positive sense ssRNA, about 7.6 kb in size, capped at the 5’ termi-
nus with m7G and polyadenylated at the 3’ terminus. The RNA accounts for about 5% of the particle
weight. Infectious cDNA clones have been produced for grapevine viruses A and B (GVA and GVB).
Proteins
The CPs are composed of a single 18–21.5 kDa polypeptide.

Genome organization and replication

The genomes contain five slightly overlapping ORFs (Figure 12). The 5’ regions of grapevine viruses
A and B initiate with an A/T-rich (60–68%) UTR of 47–86 nt. ORF1 is the replication-related pro-
tein. ORF2 is a 19–20 kDa polypeptide of unknown function with no significant sequence homol-
ogy to known proteins, which, in GVB infections, does not accumulate in phase with MPs. ORF3
(31–36.5 kDa) is the movement protein and ORF4 is the CP. The final ORF is a 10–14 kDa polypep-
tide with weak homologies to proteins with RNA-binding properties and which has been shown (in
GVA) to have RNA silencing suppressor activity.

The strategy of expression is based on sgRNA production, as suggested by the analysis of dsRNA
patterns from infected tissues. The four dsRNAs have sizes of 7.6, 6.48, 5.68 and 5.1 kbp for GVA
and GVD, and 7.6, 6.25, 5.03 and 1.97 kbp for GVB. In GVA there are nested sets of 5’-terminal
sgRNAs 5.1, 5.5 and 6.0 kb in size and of 3’-terminal sgRNAs 1.0, 1.8 and 2.2 kb that serve for
the expression of all ORFs, except for ORF5, which may be expressed via a bi- or polycistronic
mRNA. The generation of these 5’- and 3’-terminal sgRNAs appears to be controlled by inter-
nal cis-acting elements. Replication occurs in the cytoplasm, possibly in association with membra-
nous vesicles.

Antigenic properties
Virions are moderate or poor antigens. Most species are very distantly serologically related.
Monoclonal antibodies to GVA, GVB and GVD and recombinant protein antibodies to the putative

Pos. ssRNA
Grapevine virus A, GVA (7,351 nts)
10K
Mtr AlkB Hel RdRp MP NB
5′m7G A(n) 3′OH
? CP
20K
5.1 kb 5′ 3′
sgRNAs 5.5 kb 5′ 3′
6.3 kb 5′ 3′
5′ 3′ 2.2 kb

5′ 3′ 1.8 kb
sgRNAs

5′ 3′ 1.0 kb

Figure 12:  Organization and expression of the genome of grapevine virus A (GVA) showing the relative posi-
tion of the ORFs, their expression products, and the nested sets of 5’- and 3’-terminal sgRNAs. Mtr, methyl-
transferase; Hel, helicase; Pol, polymerase; MP, putative movement protein; CP, capsid protein.

935
Part II – The Positive Sense Single Stranded RNA Viruses

MP of GVA have been produced. The relationship between GVA, GVB and GVD is due to a few
common internal antigenic determinants (cryptotopes). GVA particles carry a highly structured
epitope centered in a common peptide region of the CP sequence.

Biological properties
Host range
The natural host range of individual species is restricted to a single host. Infections induce either
no symptoms (HLV and mint virus 2 (MV-2)) or severe diseases characterized by pitting and groov-
ing of the wood (GVA, GVB and GVD). The experimental host range varies from wide (HLV) to
restricted (GVA, GVB, GVD and GVE).
Transmission
All species except for MV-2 are transmitted by mechanical inoculation, those infecting grapevines
with greater difficulty. Transmission by grafting and dispersal through propagating material is com-
mon with grapevine-infecting species. GVA and GVB are transmitted in a semi-persistent manner
by different species of pseudococcid mealybugs of the genera Pseudococcus and Planococcus. GVA is
also transmitted by the scale insect Neopulvinaria innumerabilis. HLV and MV-2 are transmitted semi-
persistently by aphids, in association with a helper virus.
Geographical distribution
Geographical distribution varies from very wide (GVA, GVB, GVD) to restricted (HLV).
Cytopathic effects
Infected cells are damaged to a varying extent. All species investigated elicit the formation of vesic-
ular evaginations of the tonoplast containing finely fibrillar material, possibly representing replica-
tive forms of viral RNA. Virions of grapevine-infecting species are strictly phloem-limited, but in
herbaceous hosts they also invade the parenchyma. Virus particles accumulate in the cytoplasm in
bundles or paracrystalline aggregates.

Species demarcation criteria in the genus

The criteria demarcating species in the genus are:

l The natural host range.

l Serological specificity using discriminatory polyclonal and monoclonal antibodies.
l Epidemiology: individual species or groups of species are transmitted by different types and
species of vectors.
l Differences in dsRNA pattern.
l Less than about 72% nt identity (or 80% aa identity) between their CP or polymerase genes.

List of species in the genus Vitivirus

Grapevine virus A
  Grapevine virus A-Is 151 [X75433  NC_003604] (GVA-Is 151)
Grapevine virus B
  Grapevine virus B-Italy [X75448  NC_003602] (GVB-IT)
Grapevine virus D
  Grapevine virus D-Italy [Y07764*] (GVD-IT)
Grapevine virus E
  Grapevine virus E-Japan:TvAQ7 [AB432910  NC_011106] (GVE-TvAQ7)
Heracleum latent virus
  Heracleum latent virus-Scottish: Murant [X79270*] (HLV-MUR)
Mint virus 2
  Mint virus 2-USA [AY913795*] (MV-2-USA)
Species names are in italic script; names of isolates are in roman script. Sequence accession numbers [ ] and assigned
abbreviations ( ) are also listed.
*Sequences do not comprise the complete genome.

936
 Betaflexiviridae

List of other related viruses which may be members of the genus Vitivirus but have not
been approved as species
None reported.

List of unassigned species in the family Betaflexiviridae

African oil palm ringspot virus
  African oil palm ringspot virus-Colombia [AY072921  NC_012519] (AOPRV-COL)
Banana mild mosaic virus
  Banana mild mosaic virus-Australia [AF314662  NC_002729] (BanMMV-AUS)
Cherry green ring mottle virus
  Cherry green ring mottle virus-USA [AF017780  NC_001946] (CGRMV-USA)
Cherry necrotic rusty mottle virus
  Cherry necrotic rusty mottle virus-Germany [AF237816  NC_002468] (CNRMV-DE)
Potato virus T
  Potato virus T-Peru [EU835937  NC_011062] (PVT-Peru)
Sugarcane striate mosaic-associated virus
  Sugarcane striate mosaic-associated virus-Australia [AF315308  NC_003870] (SCSMaV-AUS)
Species names are in italic script; names of isolates are in roman script. Sequence accession numbers [ ] and assigned
abbreviations ( ) are also listed.

List of other related viruses which may be members of the family Betaflexiviridae but have
not been approved as species
Banana virus X [AY710267*] (BanVX)
White ash mosaic virus [DQ412998   NC_011533] (WAMV)
*Sequences do not comprise the complete genome.

Phylogenetic relationships within the family

In a phylogenetic analysis of the replication protein, most genera fall on well-supported branches
(Figure 13, p. 938). The family falls into two broad parts that correspond with the types of move-
ment protein. Carlavirus and Foveavirus with a number of unassigned species that have a TGB form
one branch, while the remaining genera and viruses (which all have a “30K”-type movement pro-
tein) also cluster together. Of the unassigned species, Potato virus T is expected to become the type
member of a new genus (proposed Tepovirus). The remaining unassigned species resemble foveavi-
ruses in their genome organization but do not form a monophyletic group.

Pos. ssRNA
Similarity with other taxa
The polymerase proteins are members of the “alphavirus-like” supergroup of RNA viruses
and are most closely related to those of the other families in the order, namely Alphaflexiviridae,
Gammaflexiviridae and Tymoviridae. There are also similarities between the TGB-containing genera and
members of the family Alphaflexviridae in the 3’ end of the genome (Figure 14, p. 939). The TGB pro-
teins are also more distantly related to those of rod-shaped viruses in the family Virgaviridae (genera
Hordeivirus, Pecluvirus and Pomovirus) (Figure 15a, p. 940). The “30K” movement proteins are related
to those in the family Virgaviridae (genera Furovirus, Tobamovirus and Tobravirus) (Figure 15b, p. 940).

Derivation of names
Capillo: from Latin capillus, “a hair”.
Carla: from Carnation latent virus.
Citri: from Citrus leaf blotch virus.
Flexi: from Latin flexus, “bent”.
Fovea: from Latin fovea, “pit” or “hole”, a type of symptom induced by the type species.
Tricho: from Greek thrix, “hair”.
Viti: from Vitis, generic name of the grapevine, Vitis vinifera, the host of the type species.

937
Part II – The Positive Sense Single Stranded RNA Viruses

97 HpLV AB032469
77 HpMV EU527979
100 AcLV AB051848
NCLV AM158439
100
98 PVM D14449
92 NeLV DQ098905
PotLV EU433397
CVB AB245142
99 98
DVS AJ620300
PVS AJ863509
100 PVP EU020009
100 PVP EU338239
LNRSV EU074853
Carlavirus
87 BlScV L25658
96
77 KLV FJ531634
99 LSV AJ516059
PLV DQ455582
HNNV FJ196835
85 60
PopMV AY505475
CVNV EF527260
75
RCVMV FJ685618
100
99 SLV AJ292226
NSV AM182569
SPCFV AY461421
93 GRSPaV AF057136
100 ASPV D21829 Foveavirus
91 100 PCMoV EF693898
SCSMaV AF315308
AOPRV AY072921
99
100 CGRMV AF017780 Unassigned
100 CNRMV AF237816
BanMMV AF314662
70 ACLSV M58152
100 APsCLSV AY713379
ChMLV AF170028 Trichovirus
100 PcMV DQ117579
60 CLBV AJ318061 Citrivirus
ASGV D14995
CVA X82547 Capillovirus
PVT EU835937 Unassigned
76 GVE AB432910
100 GVA X75433 Vitivirus
100 GVB X75448
BotV-F AF238884

0.2

Figure 13:  Phylogenetic (distance) tree based on the amino acid sequences of the entire replication protein of members of
the family Betaflexiviridae. A single representative isolate of each sequenced species in the family was included and the tree is
rooted with Botrytis virus F (BotV-F; genus Mycoflexivirus, family Gammaflexiviridae). Numbers on branches indicate percent-
age of bootstrap support out of 1000 bootstrap replications (when 60%). The scale indicates JTT amino acid distances. Tree
produced in MEGA4.

938
 Betaflexiviridae

ICRSV Mandarivirus
NVX
WClMV
PepMV
99 PAMV
93
CymMV
100 100 AlsVX
LeVX
100 MalMV
98 AV-3
85 NMV

Alphaflexiviridae
SMYEV
62 PhVX
99 LVX
MVX
100 FoMV Potexvirus
BaMV
100 TVX
87 67 PlAMV
86 HdRSV
CsCMV
HVX
100 PapMV
78 AltMV
ClYMV
OpVX
100 SchVX
100 ZyVX
99 CVX
PVX
LoLV Lolavirus
HNNV
PopMV
CVNV
SLV
69 PeSV
96
91 RCVMV
NSV
100 MYaV
97 SPCFV
CPMMV
KLV
90 PLV
LSV
LNRSV
Carlavirus

Betaflexiviridae
99
BlScV
99
PVS
PVP
CVB

Pos. ssRNA
DVS
PotLV
NeLV
AcLV
90 HpLV
HpMV
NCLV
63 PVM
BanMMV
SCSMaV
84 GRSPaV
100 ASPV
100 ApLV Foveavirus
PCMoV
70 AOPRV
100 CGRMV
100 CNRMV
0.1

Figure 14:  Phylogenetic (distance) tree based on the 3’-terminal nucleotide sequences of those members
of the families Betaflexiviridae and Alphaflexiviridae that have a triple gene block (TGB). The sequence used
includes the entire TGB and coat protein genes (alignment length 2466 nt). A single representative isolate
of each sequenced species in each family was used. Numbers on branches indicate percentage of bootstrap
support out of 10,000 bootstrap replications (when 60%). The scale indicates maximum composite likeli-
hood distances. Tree produced in MEGA4.

939
Part II – The Positive Sense Single Stranded RNA Viruses

Figure 15:  Phylogenetic (distance) trees

a produced in MEGA4 showing how the
Alphaflexiviridae cell-to-cell movement proteins of viruses
in the family Betaflexiviridae are related
78 RCVMV FJ685618 to those of other plant viruses. (a) Tree
95 SLV AJ292226 based on the codon-aligned nucleotide
PeSV AF354652 sequences of the first triple gene block
HNNV FJ196835 protein (TGBp1). A single representative
PopMV AY505475 isolate of each sequenced species in the
DVS AJ620300 family was included. The tree also con-
VeLV AF271218 tains similar sequences from the family
PotLV EU433397 Alphaflexiviridae and those of rod-shaped
AcLV AB051848 plant viruses collapsed into triangles, the
PVM D14449 length of which corresponds to the vari-
60 NCLV AM158439 ation found within the clade. Numbers
HpLV AB032469 on branches indicate percentage of boot-
NeLV DQ098905 Carlavirus strap support out of 10,000 bootstrap
CVB AB245142 replications (when 60%). The scale
BlScV L25658 indicates maximum composite likelihood
PVP EU020009 distances. Tree produced in MEGA4. (b)
PVS AJ863509 Tree based on the amino acid sequences
PLV DQ455582 of the “30K”-like movement protein.
66 LNRSV EU074853 A single representative isolate of each
KLV FJ531634 sequenced species in the family was
LSV AJ516059 included. The tree also contains simi-
CPMMV AF024629 lar sequences from genera in the family
CVNV EF527260 Virgaviridae collapsed into triangles, the
NSV AM182569 length of which corresponds to the vari-
SPCFV AY461421 ation found within the clade. Numbers
GRSPaV AF057136 on branches indicate percentage of boot-
100 ASPV D21829 strap support out of 1000 bootstrap repli-
99 ApLV AF318062 Foveavirus
cations (when 60%). The scale indicates
PCMoV EF693898 JTT amino acid distances.
AOPRV AY072921
95 CGRMV AF017780 Unassigned
100 CNRMV AF237816
BanMMV AF314662
99
Benyvirus
90
99
99
Hordeivirus
63 Pecluvirus Virgaviridae
84
98 Pomovirus
0.1

b HLV X79270
MV-2 AY913795
78 GVB X75448 Vitivirus
GVA X75433
66
GVE AB432910
APsCLSV AY713379
98 ACLSV M58152

96
ChMLV AF170028 Trichovirus
95 PcMV DQ117579
GINV D88448
CLBV AJ318061 Citrivirus
CVA X82547
67
72
Capillovirus
ASGV D14995
PVT EU835937 Unassigned
76 100
Tobravirus
81 Tobamovirus Virgaviridae
99 Furovirus
0.5

940
 Betaflexiviridae

Further reading
Journals and books
Adams, M.J., Antoniw, J.F., Bar-Joseph, M., Brunt, A.A., Candresse, T., Foster, G.D., Martelli, G.P., Milne, R.G., Zavriev, S.K.
and Fauquet, C.M. (2004). The new plant virus family Flexiviridae and assessment of molecular criteria for species demar-
cation. Arch. Virol., 149, 1045–1060.
Bratlie, M.S. and Drabløs, F. (2005). Bioinformatic mapping of AlkB homology domains in viruses. BMC Genomics, 6, 1–15.
Martelli, G., Adams, M.J., Kreuze, J.F. and Dolja, V.V. (2007). Family Flexiviridae: a case study in virion and genome plasticity.
Annu. Rev. Phytopathol., 45, 73–100.
Vives, M.C., Galipienso, L., Navarro, L., Moreno, P. and Guerri, J. (2001). The nucleotide sequence and genomic organization
of citrus leaf blotch virus: candidate type species for a new virus genus. Virology, 287, 225–233.

Websites
International Council for the Study of Virus and Virus-like Diseases of the Grapevine: http://www.icvg.ch.

Contributed by
Adams, M.J., Candresse, T., Hammond, J., Kreuze, J.F., Martelli, G.P., Namba, S., Pearson, M.N., Ryu, K.H., Saldarelli, P. and
Yoshikawa, N.

Pos. ssRNA

941