Novel human parechovirus from Brazil

Abstract

Human parechoviruses (HPeVs) were detected by reverse transcription-PCR in 16.1% of 335 stool samples from children <6 years of age with enteritis in Salvador, Brazil. Whole genome sequencing of 1 sample showed a novel HPeV that has been designated as HPeV8.

Figure 1

Evolutionary relationships between known parechoviruses and the new human parechovirus from this study (boldface). Phylogenetic analyses of A) complete viral protein (VP) 1, B) VP0, and C) VP3, and D) the whole nonstructural region (comprising regions P2 and P3), were constructed using the Jones-Taylor-Thornton matrix-based substitution model on an amino acid–driven alignment (pairwise deletion option). The evolutionary histories were inferred using the neighbor-joining method and are in the units of the number of amino acid substitutions per site. Relevant bootstrap values from 500 replicate trees are shown next to the branches. The scale bars show the evolutionary distance from each root. Analysis was conducted in MEGA software version 4 (www.megasoftware.net). HPeV reference strains are named in full detail; their GenBank accession numbers are not further indicated. Contemporary HPeV1 strain BNI-788st accession number was EF051629 and HPeV6 strain BNI-67 accession number was EU022171. The tree was rooted against Ljungan virus, a rodent parechovirus (GenBank accession no. EF202833). In the P2/P3 tree, branches to the Ljungan virus node have been truncated for space reasons, as indicated by dotted lines.

Figure 2

Nucleic acid identity with known parechoviruses. The near full-length genome of the new parechovirus BR/217/2006 was analyzed with SimPlot software (http://sray.med.som.jhmi.edu/SCRoftware/simplot) using a 600-bp sliding window and a step size of 10. Because of partially incomplete 5′ untranslated (UTR) region GenBank reference sequences, an approximate 400 nucleotides had to be cut from the 5′ end of all genomes. HPeV, human parechovirus. A) Nucleic acid identity, per analysis window, for strain BR/217/2006 with prototype strains. Nucleotide positions on x-axis show the center of the window. B) BootScan analysis using the same window settings. A bootstrapped phylogenetic analysis was conducted per window along the alignment. Graphs represent the percentage (bootstrap values) at which each strain cosegregates phylogenetically in the analysis window with strain BR/217/2006. Prototype strains used for comparison are shown in the inserts in each panel. A schematic representation of the parechovirus genome is given on top.