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Novel human parechovirus from Brazil.

Drexler JF, Grywna K, Stöcker A, Almeida PS, Medrado-Ribeiro TC, Eschbach-Bludau M, Petersen N, da Costa-Ribeiro-Jr H, Drosten C - Emerging Infect. Dis. (2009)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: University Hospital Prof Edgard Santos, Federal University of Bahia, Salvador, 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.

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Related in: MedlinePlus

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.
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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.

Mentions: The viral protein (VP) 1 capsid protein gene has been established for molecular typing of HPeV (3). Consensus primers for amplification and sequencing of the VP1 gene were developed. Primer sequences were VP1 forward 5′-CCATARTGYTTRTARAARCCYCT-3′ and VP1 reverse 5′-CARAAYTCDTGGGGYTCMCARATGG-3′. VP1 RT-PCR was successful in only 11 of 54 HPeV-positive samples, consistent with low RNA concentrations in most samples. Ten of the 11 sequenced samples were of known and well-characterized types (type 1, 7 samples; type 5, 2 samples; and type 6, 1 sample). These samples were not further analyzed. One sample showed a VP1 sequence that clustered with none of the known HPeV types in phylogenetic analysis (Figure 1). To determine whether this virus represented a new type, its complete genome except the first 27 nucleotides of the 5′ terminus was amplified by overlapping PCR fragments, and the full nucleotide sequence was determined as described previously (9) (GenBank accession no. EU716175).


Novel human parechovirus from Brazil.

Drexler JF, Grywna K, Stöcker A, Almeida PS, Medrado-Ribeiro TC, Eschbach-Bludau M, Petersen N, da Costa-Ribeiro-Jr H, Drosten C - Emerging Infect. Dis. (2009)

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.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2657636&req=5

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.
Mentions: The viral protein (VP) 1 capsid protein gene has been established for molecular typing of HPeV (3). Consensus primers for amplification and sequencing of the VP1 gene were developed. Primer sequences were VP1 forward 5′-CCATARTGYTTRTARAARCCYCT-3′ and VP1 reverse 5′-CARAAYTCDTGGGGYTCMCARATGG-3′. VP1 RT-PCR was successful in only 11 of 54 HPeV-positive samples, consistent with low RNA concentrations in most samples. Ten of the 11 sequenced samples were of known and well-characterized types (type 1, 7 samples; type 5, 2 samples; and type 6, 1 sample). These samples were not further analyzed. One sample showed a VP1 sequence that clustered with none of the known HPeV types in phylogenetic analysis (Figure 1). To determine whether this virus represented a new type, its complete genome except the first 27 nucleotides of the 5′ terminus was amplified by overlapping PCR fragments, and the full nucleotide sequence was determined as described previously (9) (GenBank accession no. EU716175).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: University Hospital Prof Edgard Santos, Federal University of Bahia, Salvador, 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.

Show MeSH
Related in: MedlinePlus