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. 2007 Jan;81(2):1013-21.
doi: 10.1128/JVI.00584-06. Epub 2006 Sep 27.

Analysis of a new human parechovirus allows the definition of parechovirus types and the identification of RNA structural domains

Mohammed Al-Sunaidi  1 , Cigdem H Williams, Pamela J Hughes, David P Schnurr, Glyn Stanway
Affiliations

Analysis of a new human parechovirus allows the definition of parechovirus types and the identification of RNA structural domains

Mohammed Al-Sunaidi et al. J Virol. 2007 Jan.

Abstract

Human parechoviruses (HPeV), members of the Parechovirus genus of Picornaviridae, are frequent pathogens but have been comparatively poorly studied, and little is known of their diversity, evolution, and molecular biology. To increase the amount of information available, we have analyzed 7 HPeV strains isolated in California between 1973 and 1992. We found that, on the basis of VP1 sequences, these fall into two genetic groups, one of which has not been previously observed, bringing the number of known groups to five. While these correlate partly with the three known serotypes, two members of the HPeV2 serotype belong to different genetic groups. In view of the growing importance of molecular techniques in diagnosis, we suggest that genotype is an important criterion for identifying viruses, and we propose that the genetic groups we have defined should be termed human parechovirus types 1 to 5. Complete nucleotide sequence analysis of two of the Californian isolates, representing two types, confirmed the identification of a new genetic group and suggested a role for recombination in parechovirus evolution. It also allowed the identification of a putative HPeV1 cis-acting replication element, which is located in the VP0 coding region, as well as the refinement of previously predicted 5' and 3' untranslated region structures. Thus, the results have significantly improved our understanding of these common pathogens.

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Figures

FIG. 1.
FIG. 1.
(a) Phylogenetic tree, based on the partial amino acid sequence of VP1, showing the relationship between the 54 available HPeV sequences for this region. Sequences were aligned with CLUSTALW, and the tree was constructed by the PHYML program, using the JTT model of amino acid substitution. The corresponding VP1sequences of two more distantly related parechovirues, Ljungan virus M1146 and 87-012, are included as out-groups, and the branches to the Ljungan virus nodes have been truncated for space reasons, as indicated by the dotted lines. Bootstrap values from 100 pseudoreplicates are shown for the major nodes. The HPeVs cluster into 5 genoypes, labeled types 1 to 5. (b) Alignment of the C-terminal region of VP1 showing the RGD motif, seen in 4 of the types, and well-conserved flanking residues in boldface type.
FIG. 2.
FIG. 2.
Genetic relationships between completely sequenced HPeVs. The designation of each of the types, as defined in Fig. 1a, is indicated by the number (1 to 5) on the right hand side of each tree. (a) Tree based on amino acid sequences of the P1 region. Sequences were aligned with CLUSTALW, and the tree was constructed by the PHYML program, using the JTT model of amino acid substitution. The corresponding P1 sequences of two more distantly related parechoviruses, Ljungan virus M1146 (Ljungan M) and 87-012 (Ljungan 87), are included as out-groups, and the branches to the Ljungan virus nodes have been truncated for space reasons, as indicated by the dotted lines. Bootstrap values from 100 pseudoreplicates are shown for each node. (b) Tree based on nucleotide sequences of the 3D region. Sequences were aligned with CLUSTALW, and the tree was constructed by the PHYML program, using the HKY model of nucleotide substitution and a transition/transversion ratio of 4. The corresponding 3D sequences of two more distantly related parechoviruses, Ljungan virus M1146 (Ljungan M) and 87-012 (Ljungan 87), are included as outgroups, and the branches to the Ljungan virus nodes have been truncated for space reasons, as indicated by the dotted lines. Bootstrap values from 100 pseudoreplicates are shown for each node.
FIG. 3.
FIG. 3.
SimPlot analysis of the relationship between completely sequenced HPeVs, based on nucleotide similarities of other HPeVs to T92-15 (top panel) and T75-4077 (lower panel). The Kimura 2 correction was applied, with a Ts/Tv ratio of 3, and a window of 600 nucleotides and a step of 10 nucleotides were used.
FIG. 4.
FIG. 4.
(a) Alignment of the putative CRE region of HPeV strains. < and > denote nucleotides participating in the predicted stem, and covariant residues differing from the HPeV1 sequence are shaded. U/C differences maintaining the structure are underlined. (b) MFOLD-derived structure of the HPeV1 CRE. (c) Alignment of the loop regions of CREs in picornaviruses, showing the strong conservation of the motif CAAAC.
FIG. 5.
FIG. 5.
Alignment of the 3′ UTRs of HPeVs showing the tandem repeats (shaded). < and > denote nucleotides participating in the predicted stem-loop structure.
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