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Recent developments with calicivirus phylogeny

Tamás Berke and David O. Matson
Center for Pediatric Research,
Children's Hospital of The King's Daughters and Eastern Virginia Medical School,
Norfolk, Virginia, USA

Caliciviruses (CVs) were first recognized to be a virus family distinct from picornaviruses in the 1970's. CVs are small (27-38 nm), non-enveloped viruses with a 7.2 to 8.3 Kb, polyadenylated, positive-sense, ssRNA genome. The Caliciviridae include human and animal pathogens, causing a wide variety of diseases, of which gastroenteritis is known in humans. Sequencing of the genome of prototype CVs facilitated the characterization of additional strains within the family. As complete CV genome sequences became available, five distinct patterns of genome organization were noted.

Caliciviridae and Picornaviridae, which belong to the same subphylum and genera within Picornaviridae, are well characterized. Until recently, Caliciviridae included only one genus Calicivirus containing strains with distinct structural and genomic features [1].

Phylogenetic analyses of calicivirus partial capsid genes revealed five distinct clusters within Caliciviridae corresponding to differences in genome organization [2]. In order to determine to what taxonomic level these clusters correspond, available genomic sequences of caliciviruses, prototypes of picornavirus genera, and two togavirus strains were collected. Corresponding regions of the genomes were submitted to sequence analyses. Sequences were aligned and bootstrapped for phylogenetic analyses. Distance and maximum likelihood methods in PHYLIP were used to estimate the phylogenetic relationships among strains. Analysis of the most variable genomic region (capsid gene) revealed separation of five main clusters (human small round-structured viruses, Sapporo-like human caliciviruses, hepatitis E virus, vesicular exanthem of swine virus, and lapine animal caliciviruses), and the distances corresponded to those observed among picornavirus genera. A satisfactory alignment including togavirus capsid genes could not be created. Utilizing more conserved (2C and 3D) regions for the analyses, only major groups of caliciviruses were separated with confidence, with distances comparable to those separating picornavirus genera.

The position of hepatitis E virus (HEV) has been disputed since its first linkage with the Caliciviridae. When partial genes of the polymerases of positive-strand RNA viruses were analyzed, hepatitis E virus was grouped together with alpha- and rubiviruses, distinct from the picornavirus superfamily [3]. In this study, we include sequences of representative strains from two togavirus genera and each picornavirus genus and estimate phylogenetic relationships among Caliciviridae by assessment of multiple genomic regions. The analysis in these regions included togavirus sequences and with their inclusion HEV strains moved out of the CV cluster.

Our findings support the reclassification of the Caliciviridae into distinct genera [4]. This conclusion is supported by observed differences in virion morphology, genome organization, and amino acid motifs at the sequence level. The phylogenetic position of hepatitis E virus, by analysis of non-structural genes, is outside the caliciviruses, in an uncertain taxonomic position.

Figure 1. Maximum likelihood phylogram represents the phylogenetic relationships of the capsid gene among the Caliciviridae.

Figure 2. Maximum likelihood phylogram represents the phylogenetic relationship of the partial helicase gene of hepatitis E virus in relation to three other families.

References:
1. Cubitt WD, Bradley D, Carter M, Chiba S, Estes MK, Saif L, Schaffer FL, Smith AW, Studdert MJ, Thiel HJ (1995) Caliciviridae. In: Murphy FA, Fauquet CM, Bishop DHL, Ghabrial SA, Jarvis AW, Martelli GP, Mayo MA and Summers MD (eds) The Sixth Report of the International Committee for Taxonomy of Viruses. Springer Verlag, Wien, vol 10, pp 359-363

2. Berke T, Golding B, Jiang X, Cubitt DW, Wolfaardt M, Smith AW, Matson DO (1997) Phylogenetic analysis of the Caliciviruses. J-Med-Virol 52: 419-24

3. Koonin EV (1991) The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. J-Gen-Virol 72: 2197-206

4. Pringle CR (1998) Virus Taxonomy - San Diego 1998 [Virology Division News]. Arch Virol 143: 1449-59

Abstracts from the Virus Evolution Workshop
Ardmore, OK
October 21 - 24th, 1999

Virus Evolution Workshop - Main Page
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To contact the organizers:
e-mail: mroossinck@noble.org

Dr. Marilyn Roossinck
Plant Biology Division
The Noble Foundation
P.O. Box 2180
Ardmore, OK 73402

phone: 580 224-6630