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From Alan Radford, Alvin W. Smith, Grant Hansman, Gregor Meyers, Heinz-Juergen Thiel, Ian N.
Clarke, John D. Neill, Jan Vinje, Kim Y. Green, Michael J. Studdert, Marion Koopmans, David O.
Matson, Mary K. Estes, and Nick J. Knowles, Caliciviridae. In: Andrew M.Q. King, Michael J. Adams,
Eric B. Carstens, and Elliot J. Lefkowitz, editors, Virus Taxonomy. Oxford: Elsevier, 2011, pp. 977-986.
ISBN: 978-0-12-384684-6© Copyright 2011 Elsevier Inc.
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Caliciviridae

Caliciviridae

FamilyTaxonomic structure of the family
FamilyCaliciviridae
Genus	  Vesivirus
Genus	  Lagovirus
Genus	  Norovirus
Genus	  Sapovirus
Genus	  Nebovirus

Virion properties
Morphology

Virions are non-enveloped with icosahedral symmetry. They are 27–40 nm in diameter by negativestain electron microscopy and 35–40 nm by cryo-electron microscopy (Figure 1). The capsid is composed of 90 dimers of the major structural protein VP1 arranged on a T  3 icosahedral lattice. In
noroviruses, the VP1 forms a subunit comprised of a shell and two protruding domains (Figure 1).
A characteristic feature of calicivirus capsid architecture is the 32 cup-shaped depressions at each of
the icosahedral five-fold and three-fold axes. In negative-stain virus preparations, some cup-shaped
depressions appear distinct and well defined, while in others these depressions are less prominent.

Physicochemical and physical properties

Virion Mr is about 15 106. Virion buoyant density is 1.33–1.41 g cm3 in CsCl and 1.29 g cm3 inglycerol-potassium tartrate gradients. Virion S20,w is 170–187S. Physicochemical properties havebeen established for some members of the family. Generally, caliciviruses are stable in the environment and many strains are resistant to inactivation by heat and certain chemicals (ether, chloroform
and mild detergents). Enteric caliciviruses are acid-stable.
The genome consists of a linear ssRNA molecule of 7.4–8.3 kb. A protein (VPg, 10–15 kDa) iscovalently attached to the 5-terminus of the genomic RNA and the 3-terminus is polyadenylated(Figure 2). Caliciviruses have conserved nucleotide motifs at the genomic 5-terminus and at the junction of the coding sequences for the non-structural/structural proteins. A subgenomic RNA (sgRNA)of 2.2–2.4 kb is synthesized intracellularly and is apparently VPg-linked. The gene order for several
caliciviruses was determined by transient expression and in vitro translation studies and cleavage
mapping yielding at least six mature non-structural proteins, followed by two structural proteins(VP1 and VP2). All the non-structural proteins are encoded by a large polyprotein and expressed in
the same order for each genus (Figure 2). In the case of lagoviruses, sapoviruses and neboviruses theopen reading encoding the non-structural proteins is in-frame and contiguous with VP1.

Figure 1: The structure of the calicivirus capsid exemplified by cryo-image reconstruction of recombinant
Norwalk virus (NV)-like particles (rNV VLPs) (Left). X-ray structure of the Norwalk virus capsid (Right) with
the Shell, Protruding 1, and Protruding 2 domains colored in blue, red and yellow, respectively. (Courtesy of
B.V. Prasad.)

Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses© 2012 International Committee on Taxonomy of Viruses. Published by Elsevier Inc. All Rights Reserved.

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Nucleic acid

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Part II – The Positive Sense Single Stranded RNA Viruses
ORF1

Vesivirus
Norovirus

N-terminal NTPase 3A-like VPg Protease

ORF2
Polymerase

VP1 Capsid

ORF3
VP2
A(n) 3′OH

VPg

Lagovirus
Sapovirus
Nebovirus

ORF1
N-terminal NTPase 3A-like VPg Protease

ORF2
Polymerase

VP1 Capsid

VP2
A(n) 3′OH

VPg

Subgenomic RNA(All genera)

VP1 Capsid
VPg

VP2
A(n) 3′OH

Figure 2: Reading frame usage and gene order in the Caliciviridae. Caliciviruses have a positive-strand RNA
genome (7.4–8.3 kb), depicted by the horizontal black lines, which carry a protein (VPg) covalently linked to
the 5-terminus. The genome also contains a characteristic, short repeated sequence (❚) at the 5-terminus andat the start of the VP1 gene. The genome (of each genus as indicated) is organized into at least two or threemajor ORFs as indicated. Structural genes are shown as pink (VP1) and blue (VP2) and the VPg gene is shownas green. In all genera, the structural proteins VP1 and VP2 are produced during replication from an abundant
subgenomic RNA transcript that is co-terminal with the 3-terminus of the genome. The ORF1 cleavage events
mediated by the viral cysteine protease vary among the genera, but the gene order of the nonstructural proteins is conserved. Conserved cleavage sites are indicated with a solid vertical line; cleavage sites that vary inusage among genera are indicated with a broken vertical line. (Re-designed by Rachel Skilton.)

Proteins

Virions are predominantly comprised from one major capsid protein, VP1 (58–60 kDa). A second
minor structural protein named VP2 (8.5–23 kDa) has been found in association with FCV and
RHDV virions, and Norwalk virus-like particles. Some non-structural proteins have sequenceand motif homology with those of the family Picornaviridae replicative enzymes and include 2C(NTPase), 3C (cysteine protease) and 3D (RNA-dependent RNA polymerase) domains. The calici­
virus VPg (10–15 kDa) is covalently linked to the viral RNA and maps to the region of the calicivirus
genome analogous to the 3B region of picornaviruses, but without having an apparent amino acidhomology with those of picornaviruses (Figure 2).

LipidsNone reported.

Carbohydrates
None reported.

Genome organization and replication
Caliciviruses have single stranded, positive sense genomic RNA (positive-strand RNA) organized into either two or three major ORFs (see genus descriptions). The non-structural proteins are
encoded in the 5-terminus of the genome and the structural proteins in the 3-terminus (Figure 2).
Replication occurs in the cytoplasm and two major positive-strand RNA species are found in
infected cells: (1) the genome-sized, positive-strand RNA serves as the template for translation ofa large polyprotein that undergoes cleavage by a virus-encoded protease to form the mature nonstructural proteins and (2) a subgenomic-sized, positive-strand RNA, co-terminal with the 3- terminus of the genome is the template for translation of the VP1 as well as the 3-terminal ORF product
VP2. A dsRNA corresponding in size to full-length genomic RNA has been identified in FCV andSan Miguel sea lion virus (SMSV)-infected cells, indicating that replication occurs via a negativestrand intermediate.

Antigenic properties
Taking each genus in turn, the prototype virus for the vesiviruses is vesicular exanthema of swine
virus (VESV) isolated from pigs and 13 serotypes are recognized by serum neutralization assays.
Following the isolation of SMSV, which is the progenitor of VESV, additional vesivirus serotypes

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Caliciviridae
were recovered from at least 28 marine and other species. These viruses (now more than 40 serotypes) have been grouped together phylogenetically as the “marine vesiviruses”. FCV represents
the second species within the vesiviruses. Although initial studies of FCV indicated there were multiple serotypes, examinations of large collections of viruses and feline antisera obtained from experimental infections in specific pathogen-free cats led to recognition of extensive cross-reactions and aconsensus that FCV represents a single serotype, albeit with antigenic variants.
Within the lagoviruses, cross-challenge studies in the natural host and experiments with monoclonal antibodies indicate that RHDV and European brown hare syndrome virus (EBHSV) are antigenically distinct.
Antigenic types have been defined by cross-challenge studies, immune electron microscopy orsolid phase immune electron microscopy for non-cultivatable viruses in the genera Norovirus andSapovirus. By contrast, viruses in the Nebovirus genus appear to fall into a single, closely related antigenic grouping.
For some non-cultivable viruses that are members of the genera Lagovirus, Norovirus and Sapovirus,
recombinant virus-like particles (rVLPs) can be produced by expression of VP1 in mammalian,
insect and plant systems. These VLPs are highly immunogenic and similar in antigenicity to native
virions and they are useful to study the structure and antigenicity of virus particles.

Biological properties
Caliciviruses have been isolated from a broad range of vertebrates. Except for some vesiviruses,
individual caliciviruses generally exhibit a natural host restriction and this has presented a considerable problem with studying specific viruses for which there is no productive cell culture system,e.g. human noroviruses. However, at least one example virus from each genus can now be cultivated except for the neboviruses.

Transmission of caliciviruses is via direct contact with an infected host or indirectly via contact with
faecal material, vomitus or respiratory secretions, contaminated food, water and fomites. In general,
no biologic vectors appear to be involved in transmission, however, mechanical, arthropod vectortransmission of RHDV and VESV has been described.
Caliciviruses are associated with a number of disease syndromes. Marine vesiviruses (e.g. VESV)
produced clinical signs in swine that were indistinguishable from foot-and-mouth disease, andinclude vesicles in the mouth, tongue, lips, snout and feet at the coronary band and between thedigits. In addition, the virus may cause encephalitis, myocarditis, fever, diarrhoea, abortion, hepatitis, pneumonia and hemorrhage and failure of recovered animals to thrive. FCV in cats is predominantly associated with oral ulceration and rhinitis, and causes persistent infections. Recently, a more
severe disease termed virulent-systemic feline calicivirus disease has been recognized, associatedwith epithelial cytolysis and systemic vascular compromise in susceptible cats, leading to severe
oedema and high mortality.
In the genus Lagovirus, RHDV is associated with a generalized viraemic infection in which there
is massive liver necrosis that triggers a disseminated intravascular coagulation and rapid deathin rabbits greater than three months of age. Non-virulent viruses related to RHDV have been
described. EBHSV is similar to RHDV but appears to be less virulent.

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The marine vesiviruses have both a broad host range and a wide cell tropism. The diversity in hostspecies of the marine vesiviruses was not initially recognized. For example, the VESVs isolated
from swine from 1932 through 1956 were considered swine viruses and those subsequently isolated
from ocean or other sources were either designated SMSVs or named after the original host species from which they were first isolated (e.g. walrus, cetacean, reptile). All these marine vesiviruses
including those isolated from bystander host species are closely related genetically and generally
lack host specificity.

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Part II – The Positive Sense Single Stranded RNA Viruses
Human caliciviruses in the genera Norovirus and Sapovirus induce a generally self-limiting gastroenteritis. Vomiting is a consistent and prominent symptom; other symptoms may include nausea,
diarrhoea, abdominal cramping, fever and malaise. Prolonged disease is seen in immunocompromised individuals. Neboviruses cause diarrhoea and mild upper intestinal lesions in calves.

Genus

Vesivirus

Type species

Vesicular exanthema of swine virus

Distinguishing features
The species in this genus form a distinct clade within the family (Figure 3). The genome is organized into three major ORFs. ORF1 encodes the non-structural polyproteins. ORF2 encodes the
major structural capsid protein that is translated as a larger precursor protein before cleavage into
the mature VP1, a feature that appears unique to this genus. ORF1 and ORF2 of the viruses in thisgenus are separated by either 2 nt (GC for FCV strains) or 5 nt (CCACT/C for marine vesiviruses).
A third ORF (ORF3) encodes VP2 a small, basic protein and overlaps by one nt with ORF2 in a 1
frameshift. The ORF3 product has been detected in FCV-infected cells and is essential for infectious
virus production.

Biological properties
Most members of this genus can be readily propagated in cell culture. FCV grows most efficiently
in cells of feline origin; in vivo, the primary site of replication is the upper respiratory tract. Primaryisolation of most marine vesiviruses is possible in African green monkey kidney or porcine kidneycells. When tested approximately half of marine vesiviruses have produced skin vesicles in swine,
horses and sometimes cattle and vesicles have occurred naturally in dogs, pinnipeds, cetaceans andprimates (including man).

Species demarcation criteria in the genus
Members of a Vesivirus species share a major phylogenetic branch within the genus and a common
genome organization, however, demarcation into two species is on the basis of phylogenetic differences, subtle variation in genome structure and host range.
The virus VESV A48 is the prototype virus of the genus Vesivirus. This virus and those isolated frommarine species are phylogenetically grouped together and colloquially referred to as “marine vesiviruses”. Feline calicivirus (FCV) is also recognized as a separate species within the genus. A collection of representative vesivirus isolates from which some sequences have been used to generate
Figure 3 are shown in the table below.

List of species in the genus Vesivirus
Feline calicivirus
Feline calicivirus [CFI/68]
Vesicular exanthema of swine virus
Vesicular exanthema of swine virus A48 [Fontana/48][U13992](FCV)[U76874](VESV-A48)

Species names are in italic script; names of isolates are in roman script. Sequence accession numbers [ ] and assigned
abbreviations ( ) are also listed.
Full table with more complete list of virus isolates can be found online on Science Direct®, www.sciencedirect.com.

List of other related viruses which may be members of the genus Vesivirus but have notbeen approved as species
Canine calicivirus [No. 48]
2117 CHOcalicivirus
Mink calicivirus [MV-20]

980[AB070225][AY343325][AF338407](CaCV)(2117)(MCV)

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Caliciviridae

Genus

Lagovirus

Type species

Rabbit hemorrhagic disease virus

Distinguishing features
The strains in this genus form a distinct clade within the family. The genome is organized into two
major ORFs. ORF1 encodes the non-structural polyprotein, with the major structural protein gene
(VP1) in frame with the non-structural polyprotein coding sequence. The translated region of ORF2
overlaps ORF1 by 5 nt in the RHDV genome and 5 nt in the EBHSV genomes. The ORF2 encodes asmall protein (VP2) of unknown function that has been identified as a minor structural component
in the RHDV virion.

Biological properties
These viruses have characteristically been associated with infection in rabbits and hares (lagomorphs), and can cause epidemics with high mortality in these animals. There is no productive continuous cell culture system for lagoviruses but recently infection of a rabbit kidney cell line withRHDV has been reported.

Species demarcation criteria in the genus
Members of a Lagovirus species, either RHDV or EBHSV, share a major phylogenetic branch within
the genus, common genome organization, natural host range and cross-protection antigens.
Examples of lagoviruses are shown in Table 3.

List of species in the genus Lagovirus
European brown hare syndrome virus
EBHSV [FRG]
Rabbit hemorrhagic disease virus
RHDV [FRG/89][U09199](EBHSV-FRG)[M67473](RHDV-FRG)

Species names are in italic script; names of isolates are in roman script. Sequence accession numbers [ ] and assigned
abbreviations ( ) are also listed.
Full table with more complete list of virus isolates can be found online on Science Direct®, www.sciencedirect.com.

Pos. ssRNA

List of other related viruses which may be members of the genus Lagovirus but have notbeen approved as species
None reported.

Genus

Norovirus

Type species

Norwalk virus

Distinguishing features
The strains in this genus form a distinct clade within the family. The full-length genome sequence
is available for many strains (100). The first complete genomes to be sequenced were for Norwalk
virus, Southampton virus and Lordsdale virus and showed that the genome is organized into threemajor ORFs. ORF1 encodes the non-structural polyprotein. ORF2 encodes the major structural capsid protein (VP1) and overlaps by 14 nt with ORF1 in the Norwalk and Southampton virus strains
and by 17 nt in the Lordsdale virus strain, resulting in a 2 frameshift of ORF2 in all three viruses.
ORF3 overlaps by one nt with ORF2 in a 1 frameshift and encodes a small virion-associated protein (VP2). Detailed phylogenetic analysis indicated there are at least five “genogroups” (labelled GI
to GV). Examples of the key viruses that form the genogroups are shown in Figure 3 and are listed
below. Genogroup I (GI) is made up of eight genotypes, GII contains 19 genotypes, GIII and GIV
each have two genotypes and GV has only one.

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Biological properties
Noroviruses have been detected in several mammalian species. Human noroviruses belong to GI,
GII and GIV. Porcine (GII), bovine and ovine noroviruses (GIII) have been described and murine
noroviruses currently constitute GV. However, serological evidence suggests other rodent noro­viruses exist and thus viruses in GV are likely not to be exclusively murine in origin. At present
only murine noroviruses can be grown in cell culture. Other mammalian species can be experimentally infected with human noroviruses. Furthermore, noroviruses closely related to human noro­viruses have been identified from other mammalian species, but it is not clear whether these are
the natural hosts or bystanders that have become naturally infected. Recombination between
viruses in the same genotype and between genogroups occurs.

Species demarcation criteria in the genus
Not applicable as only one species is currently recognized. However, the range of host species andthe nature and extent of diversity of the noroviruses will need further characterization to delineate
species criteria.

List of species in the genus Norovirus
There is only one species, Norwalk virus, however, representatives of each genogroup are shown
below:
Norwalk virus
GI [Hu/Norwalk virus 8FiiA/68/US]
GII [Hu/Hawaii virus/1971/US]
GIII [Bo/Jena/1980/GE]
GIV [Hu/Alphatron/98-2/1998/NL]
GV [Mu/Murine norovirus 1/2002/US][M87661][U07611][AJ011099][AF195847][AY228235](GI-NV)(GII-HV)(GIII-Jena)(GIV-Alphatron)(GV-MNV1)

Species names are in italic script. Names of genogroups (G) followed by representative virus designations are in roman script.
Host abbreviations are: Hu, human: Bo, bovine. Sequence accession numbers [ ] and assigned abbreviations ( ) are also listed.
Full table with more complete list of virus isolates can be found online on Science Direct®, www.sciencedirect.com.

List of other related viruses which may be members of the genus Norovirus but have notbeen approved as species
None reported.

Genus

Sapovirus

Type species

Sapporo virus

Distinguishing features
The viruses in this genus form a distinct clade within the family. The first full-length genomic
sequence available was for the human virus Manchester virus and subsequently for a range ofviruses including the “porcine enteric calicivirus” (PEC strain Cowden). The Manchester virus
genome is organized into three ORFs, two with known function. ORF1 encodes the non-structural polyprotein together with the major structural capsid protein gene (VP1) in frame with thenon-structural polyprotein coding sequence. In PEC, ORF2 overlaps ORF1 in a 1 frameshift andencodes a predicted small protein likely the equivalent of VP2 in noroviruses. ORF3 begins 11 nt
downstream from the predicted start codon of the VP1 in a 1 frameshift and encodes a predicted
protein of ~160 aa. In some strains of this genus, and in the PEC Cowden strain, ORF3 is absent.
Viruses in the genus are highly heterogeneous and can be divided on the basis of phylogenetic analysis of VP1 into five genogroups; GI, GII, GIV and GV contain human sapoviruses whereas porcine
sapoviruses are found only in GIII (Figure 3). Each sapovirus genogroup can be subdivided into
numerous genotypes. Examples of sapoviruses representing the genogroups are shown below.

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Caliciviridae

Biological properties
None of the human sapoviruses can be propagated in cell culture. However, PEC can be grown in
porcine kidney cells as long as the media is supplemented with bile salts to induce intracellularsignals to permit virus replication. Sapovirus infection most commonly occurs in children under
the age of 5 years and is especially characterized by outbreaks in closed settings. However, recent
molecular epidemiological studies have suggested that the number of outbreaks in which individuals of all age groups are infected may be increasing. Expression of VP1 in recombinant systems
usually results in the production of VLPs. Antiserum raised against these VLPs and cross-reactivity
studies using these VLPs and antiserum suggests that the antigenic differences amongst sapoviruses mirror the phylogenetic differences observed by genogrouping. Inter-genogroup and intragenogroup recombination has been documented.

List of species in the genus Sapovirus
The prototype strain for the species is the Sapporo virus, however, there is only a partial genome
sequence available for this virus. Other representative viruses (one for each genogroup) are shown
below.
Sapporo virus
GI [Hu/Sapporo/1982/JP]
GI [Hu/Manchester/1993/UK]
GII [Hu/Bristol/1998/UK]
GIII [Po/PEC Cowden]
GIV [Hu/Hou7-1181/1990/US]
GV [Hu/Arg39/1995/ARG][U65427][X86560][AJ249939][AF182760][AF435814][AY289803](GI-SV)(GI-Man)(GII-Bristol)(GIII-Cowden)(GIV-Houston)(GV-Arg39)

Species names are in italic script. Names of genogroups (G) followed by representative virus designations are in roman
script. Host abbreviations are: Hu, human; Po, swine. Sequence accession numbers [ ] and assigned abbreviations ( )are also listed. The genome sequence for Sapporo virus is only partial, therefore the first complete sapovirus genome
sequence is for Manchester virus.
Full table with more complete list of virus isolates can be found online on Science Direct®, www.sciencedirect.com.

List of other related viruses which may be members of the genus Sapovirus but have notbeen approved as species

Genus

Nebovirus

Type species

Newbury-1 virus

Distinguishing features
The viruses in this genus have been detected only in calves thus far and they form a distinct
clade within the family. The complete genome sequence is available for several strains including
Newbury “agent”-1, the prototype virus from the UK, and BEC-NB (Nebraska) virus describedin the USA. The nebovirus genome is organized into two major ORFs. ORF1 encodes the nonstructural polyprotein, with the major structural capsid protein (VP1) gene in frame with the nonstructural polyprotein. VP2 is frameshifted 2 and begins 2 nts after the termination of ORF1.

Biological properties
Neboviruses have been known since the 1980s but constitute the most recently defined calicivirus
genus. They cause endemic diarrhoeal disease in calves and the severity of disease in experimentally infected calves is considered equal or worse than that caused by genogroup 3 bovine noroviruses. Neboviruses cannot be grown in cell culture and therefore information on their biologicalproperties is limited. There appear to be two phylogenetically distinct polymerase types but the
VP1 sequence is conserved between the prototype viruses, Newbury agent 1 and BEC NB virus.
This suggests that, like other enteric caliciviruses, neboviruses may also undergo recombination.

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None reported.

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Species demarcation criteria in the genus
Not applicable as only one species is currently recognized. Additional characterization of theviruses in this genus will be required in order to delineate species criteria.

List of species in the genus Nebovirus
Newbury-1 virus
Newbury-1 virus UK-1976
Bovine calicivirus CV23-OH[DQ013304][AY082890](Newbury1)(CV23-OH)

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 Nebovirus but have notbeen approved as species
None reported.

List of unassigned species in the family Caliciviridae
None reported.

List of other related viruses which may be members of the family Caliciviridae but havenot been approved as species
In 2008, a positive-strand RNA virus (Tulane virus) was isolated from stool samples taken from rhesus macaques held in captivity. The genome sequence and organisation (three ORFs) of this virus
show the characteristic structure of caliciviruses (as defined in Figure 2) although with 6714 nt it
is some 600 nt shorter than previously described calicivirus genomes. Whilst Tulane virions sharesimilar morphology and density (1.7 g cm3) to other caliciviruses, phylogenetic analysis of theTulane virus genome placed it on a deeply rooted branch separate from the other calicivirus genera.
Although no disease entity has been associated with the Tulane virus, it appears to be an entericvirus and is cultivatable in a continuous macaque kidney cell line. The genus name Recovirus (forrhesus enteric calicivirus) has been proposed within the scientific literature with Tulane virus as the
prototype.
In 2009 a report described a novel calicivirus isolated from pigs in Quebec, Canada. Genomic analysis revealed a positive sense genome of 6409 nt encoding two major ORFs. Phylogenetic analysis
showed that these viruses form a unique cluster with a common root with the noroviruses and theTulane virus. The genus name Valovirus was proposed with the St-Valérien virus as the prototype.
In October 2010 the complete genome sequence of a chicken calicivirus was submitted to the public
databases. Analysis of this sequence suggests that it may form a novel calicivirus species and genus.
Tulane virus
St-Valérien virus
Chicken calicivirus[EU391643][FJ355928][HQ010042](TulaV)(ValoV)(ChCV)

Phylogenetic relationships within the family
There are five recognized genera within the family Caliciviridae. The phylogenetic relationships
amongst them are summarized in Figure 3.

Similarity with other taxa
Caliciviruses have some properties similar to the viruses in the order Picornavirales and family
Potyviridae in that they possess a genome-linked protein, VPg, at the 5-terminus and a poly(A) tract
at the 3-terminus of the genome. The viral RNA-dependent RNA polymerase and the protease of
caliciviruses share sequence homology with the picornaviruses.

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Caliciviridae
Norovirus
Hu/Chiba
Hu/Hawaii
Ca/Bari
Ca/Viseu
Sw/918
Hu/Lordsdale
Hu/FtLauderdale
Bo/Jena
Hu/Alphatron
Ov/Norsewood
Mu/MNV
Bo/Newbury2
Po/Brazil
Hu/Southampton
Po/OHJJ681
Hu/Norwalk
Po/SaV1
La/RHDV-FRG
Po/CaV
Lagovirus
La/EBHSV-BS89
Hu/Bristol98
Bo/Newbury1
Hu/London
Nebovirus
Bo/CV23OH
Hu/Angelholm
Fe/FCV68
Hu/Houston7-1181
Fe/FCV9
Hu/NongKhai24
A48
Po/VESVSapovirus
Hu/Arg39
Pi/SMSV4
Po/0618p3
Pi/SMSV17
Po/F1910
Pa/Pan1
Hu/Manchester
Pi/WCV
Vesivirus
Hu/Sapporo
CHO/CaV Ca/CaV Pi/SMSV1
0.1

Figure 3: Phylogenetic relationships in the family Caliciviridae. The noroviruses are highlighted in red, lago­viruses in light blue, neboviruses in yellow, vesiviruses in green and sapoviruses in blue. Two prototype
viruses were included to represent each genogroup, For some genera, additional strains were included to demonstrate circulation in different species (e.g., Po/Sw917 in norovirus GII). Genera are defined by amino acidp-distance of up to 0.7, genera cut-offs were expanded to include all representative genogroups within a genus.
The amino acids of full length VP1 capsid sequences were aligned in SeaView 4.2 using MUSCLE with a gap
cost of 5 and neighbor-joining clustering method for the 1st and 2nd iterations. Bayesian phylogenetic analysis was run on BEAST without a molecular clock for 106 iterations using the WAG amino acid substitution andYule speciation tree model. Parameters and length of the run was verified by using Tracer, part of the BEAST
suite of programs. All genera are supported by posterior distribution value of 1.0 (100% of sampled trees). The
scale bar represents amino acid substitutions per site. (Courtesy of Everardo Vega.)

Calici: from Latin calix, “cup” or “goblet”, from cup-shaped depressions on the virion surface
observed by electron microscopy.
Vesi: from the type species name vesicular exanthema of swine virus.
Lago: from Lagomorpha, the mammalian host order for the prototype strain rabbit haemorrhagic
disease virus.
Noro: modified from the type species name Norwalk virus.
Sapo: modified from the type species name Sapporo virus.
Nebo: derived by using the first two letters from Newbury and Nebraska, the first two isolates tobe studied together with bo for bovine the only host species from which these viruses have been
described.

Further reading
Farkas, T., Zhong, W.M., Jing, Y., Huang, P.W., Espinosa, S.M., Martinez, N., Morrow, A.L., Ruiz-Palacios, G.M., Pickering,
L.K. and Jiang, X. (2004). Genetic diversity among sapoviruses. Arch Virol., 149, 1309–1323.
Farkas, T., Sestak, K., Wei, C. and Jiang, X. (2008). Characterization of a rhesus monkey calicivirus representing a new genus
of Caliciviridae. J. Virol., 82, 5408–5416.
Glass, R.I., Parashar, U.D. and Estes, M.K. (2009). Norovirus gastroenteritis. N. Engl. J. Med., 361, 1776–1785.
Green, K.Y. (2007). Caliciviridae: The Noroviruses. In: D.M. Knipe and P.M. Howley (Eds.), Fields Virology (pp. 949–980).
Philadelphia: Lippincott Williams & Wilkins, Wolters Kluwer Business.
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Derivation of names

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Part II – The Positive Sense Single Stranded RNA Viruses
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Contributed by
Clarke, I.N., Estes, M.K., Green, K.Y., Hansman, G.S., Knowles, N.J., Koopmans, M.K., Matson, D.O., Meyers, G., Neill, J.D.,
Radford, A., Smith, A.W., Studdert, M.J., Thiel, H.-J. and Vinjé, J.

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