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A novel bocavirus associated with acute gastroenteritis in Australian children.

Arthur JL, Higgins GD, Davidson GP, Givney RC, Ratcliff RM - PLoS Pathog. (2009)

Bottom Line: Fecal samples collected from case control pairs during 2001 for the AGE study were tested with a bocavirus-specific PCR, and HBoV2 (sequence confirmed) was detected in 32 of 186 cases with AGE (prevalence 17.2%) compared with only 15 controls (8.1%).During the course of this screening, a second novel bocavirus was detected which we have designated HBoV species 3 (HBoV3).The prevalence of HBoV3 was low (2.7%), and it was not associated with AGE.

View Article: PubMed Central - PubMed

Affiliation: Infectious Diseases Laboratories, Institute of Medical and Veterinary Science, Adelaide, Australia. jane.arthur@imvs.sa.gov.au

ABSTRACT
Acute gastroenteritis (AGE) is a common illness affecting all age groups worldwide, causing an estimated three million deaths annually. Viruses such as rotavirus, adenovirus, and caliciviruses are a major cause of AGE, but in many patients a causal agent cannot be found despite extensive diagnostic testing. Proposing that novel viruses are the reason for this diagnostic gap, we used molecular screening to investigate a cluster of undiagnosed cases that were part of a larger case control study into the etiology of pediatric AGE. Degenerate oligonucleotide primed (DOP) PCR was used to non-specifically amplify viral DNA from fecal specimens. The amplified DNA was then cloned and sequenced for analysis. A novel virus was detected. Elucidation and analysis of the genome indicates it is a member of the Bocavirus genus of the Parvovirinae, 23% variant at the nucleotide level from its closest formally recognized relative, the Human Bocavirus (HBoV), and similar to the very recently proposed second species of Bocavirus (HBoV2). Fecal samples collected from case control pairs during 2001 for the AGE study were tested with a bocavirus-specific PCR, and HBoV2 (sequence confirmed) was detected in 32 of 186 cases with AGE (prevalence 17.2%) compared with only 15 controls (8.1%). In this same group of children, HBoV2 prevalence was exceeded only by rotavirus (39.2%) and astrovirus (21.5%) and was more prevalent than norovirus genogroup 2 (13.4%) and adenovirus (4.8%). In a univariate analysis of the matched pairs (McNemar's Test), the odds ratio for the association of AGE with HBoV2 infection was 2.6 (95% confidence interval 1.2-5.7); P = 0.007. During the course of this screening, a second novel bocavirus was detected which we have designated HBoV species 3 (HBoV3). The prevalence of HBoV3 was low (2.7%), and it was not associated with AGE. HBoV2 and HBoV3 are newly discovered bocaviruses, of which HBoV2 is the thirdmost-prevalent virus, after rotavirus and astrovirus, associated with pediatric AGE in this study.

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The HBoV2 and HBoV3 genomes.Diagrammatic representation of HBoV2 (HBoV2-W153, 5204 nucleotides) and HBoV3 (HBoV3-W471, 5242 nucleotides) sequence showing the position of open reading frames for NS1, NP1, VP1, and VP2, compared with other bocaviruses: bovine parvovirus 1 (BPV 1), minute virus of canines (MVC), and human bocavirus (HBoV). For both HBoV2 and HBoV3, as with HBoV, the NP1 gene is in an alternate reading frame to VP1 and overlaps the start of VP1 by 13 nucleotides. Similarly, VP2 is collinear to VP1 and results from initiation of translation at a downstream ATG and co-terminates.
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ppat-1000391-g002: The HBoV2 and HBoV3 genomes.Diagrammatic representation of HBoV2 (HBoV2-W153, 5204 nucleotides) and HBoV3 (HBoV3-W471, 5242 nucleotides) sequence showing the position of open reading frames for NS1, NP1, VP1, and VP2, compared with other bocaviruses: bovine parvovirus 1 (BPV 1), minute virus of canines (MVC), and human bocavirus (HBoV). For both HBoV2 and HBoV3, as with HBoV, the NP1 gene is in an alternate reading frame to VP1 and overlaps the start of VP1 by 13 nucleotides. Similarly, VP2 is collinear to VP1 and results from initiation of translation at a downstream ATG and co-terminates.

Mentions: Homology alignments with selected members of the Parvovirinae, including all members of the genus Bocavirus (bovine parvovirus 1, minute virus of canines and HBoV), confirm that W153 is a member of the Bocavirus genus of the Parvovirinae (Figure 1). From this alignment we predict that the W153 sequence spans the entire coding region of the virus genome but lacks up to 100 nucleotides of both terminal regions. At the nucleotide level the W153 sequence is 23% variant from its closest relative, the HBoV but contains open reading frames (ORFs) for NS1, NP1, VP1 and VP2 proteins in a similar arrangement to the HBoV including the alignment of the NP1 ORF in an alternate reading frame to VP1 whereby it overlaps the start of the VP1 by 13 nucleotides (Figure 2). A comparison of the length of the coding regions, and the genetic distance (percent dissimilarity) between them, for W153 and HBoV at the nucleotide and amino acid level are presented in Table 1. These results are in contrast to strains of the HBoV where the homology between all strains exceeds 98% at both nucleotide and amino acid level for all ORFs [24],[31]. The ICTVb criteria for defining a new species in the bocavirus genus is a non-structural gene genetic homology of less than 95% (C. Büchen-Osmond, International Committee on Taxonomy of Viruses, http://www.ncbi.nlm.nih.gov/ICTVdb/Ictv/fs_parvo.htm, Columbia University, New York, USA). Thus we propose that the virus detected in sample W153 is not a new strain of the HBoV but rather a new species of Bocavirus (family Parvoviridae subfamily Parvovirinae) and have assigned the name Human Bocavirus species 2 (HBoV2; see Discussion and reference 35 for further details). The sequence of the HBoV2-W153 strain has been deposited in GenBank (designated HBoV2-W153, accession number EU082213).


A novel bocavirus associated with acute gastroenteritis in Australian children.

Arthur JL, Higgins GD, Davidson GP, Givney RC, Ratcliff RM - PLoS Pathog. (2009)

The HBoV2 and HBoV3 genomes.Diagrammatic representation of HBoV2 (HBoV2-W153, 5204 nucleotides) and HBoV3 (HBoV3-W471, 5242 nucleotides) sequence showing the position of open reading frames for NS1, NP1, VP1, and VP2, compared with other bocaviruses: bovine parvovirus 1 (BPV 1), minute virus of canines (MVC), and human bocavirus (HBoV). For both HBoV2 and HBoV3, as with HBoV, the NP1 gene is in an alternate reading frame to VP1 and overlaps the start of VP1 by 13 nucleotides. Similarly, VP2 is collinear to VP1 and results from initiation of translation at a downstream ATG and co-terminates.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2663820&req=5

ppat-1000391-g002: The HBoV2 and HBoV3 genomes.Diagrammatic representation of HBoV2 (HBoV2-W153, 5204 nucleotides) and HBoV3 (HBoV3-W471, 5242 nucleotides) sequence showing the position of open reading frames for NS1, NP1, VP1, and VP2, compared with other bocaviruses: bovine parvovirus 1 (BPV 1), minute virus of canines (MVC), and human bocavirus (HBoV). For both HBoV2 and HBoV3, as with HBoV, the NP1 gene is in an alternate reading frame to VP1 and overlaps the start of VP1 by 13 nucleotides. Similarly, VP2 is collinear to VP1 and results from initiation of translation at a downstream ATG and co-terminates.
Mentions: Homology alignments with selected members of the Parvovirinae, including all members of the genus Bocavirus (bovine parvovirus 1, minute virus of canines and HBoV), confirm that W153 is a member of the Bocavirus genus of the Parvovirinae (Figure 1). From this alignment we predict that the W153 sequence spans the entire coding region of the virus genome but lacks up to 100 nucleotides of both terminal regions. At the nucleotide level the W153 sequence is 23% variant from its closest relative, the HBoV but contains open reading frames (ORFs) for NS1, NP1, VP1 and VP2 proteins in a similar arrangement to the HBoV including the alignment of the NP1 ORF in an alternate reading frame to VP1 whereby it overlaps the start of the VP1 by 13 nucleotides (Figure 2). A comparison of the length of the coding regions, and the genetic distance (percent dissimilarity) between them, for W153 and HBoV at the nucleotide and amino acid level are presented in Table 1. These results are in contrast to strains of the HBoV where the homology between all strains exceeds 98% at both nucleotide and amino acid level for all ORFs [24],[31]. The ICTVb criteria for defining a new species in the bocavirus genus is a non-structural gene genetic homology of less than 95% (C. Büchen-Osmond, International Committee on Taxonomy of Viruses, http://www.ncbi.nlm.nih.gov/ICTVdb/Ictv/fs_parvo.htm, Columbia University, New York, USA). Thus we propose that the virus detected in sample W153 is not a new strain of the HBoV but rather a new species of Bocavirus (family Parvoviridae subfamily Parvovirinae) and have assigned the name Human Bocavirus species 2 (HBoV2; see Discussion and reference 35 for further details). The sequence of the HBoV2-W153 strain has been deposited in GenBank (designated HBoV2-W153, accession number EU082213).

Bottom Line: Fecal samples collected from case control pairs during 2001 for the AGE study were tested with a bocavirus-specific PCR, and HBoV2 (sequence confirmed) was detected in 32 of 186 cases with AGE (prevalence 17.2%) compared with only 15 controls (8.1%).During the course of this screening, a second novel bocavirus was detected which we have designated HBoV species 3 (HBoV3).The prevalence of HBoV3 was low (2.7%), and it was not associated with AGE.

View Article: PubMed Central - PubMed

Affiliation: Infectious Diseases Laboratories, Institute of Medical and Veterinary Science, Adelaide, Australia. jane.arthur@imvs.sa.gov.au

ABSTRACT
Acute gastroenteritis (AGE) is a common illness affecting all age groups worldwide, causing an estimated three million deaths annually. Viruses such as rotavirus, adenovirus, and caliciviruses are a major cause of AGE, but in many patients a causal agent cannot be found despite extensive diagnostic testing. Proposing that novel viruses are the reason for this diagnostic gap, we used molecular screening to investigate a cluster of undiagnosed cases that were part of a larger case control study into the etiology of pediatric AGE. Degenerate oligonucleotide primed (DOP) PCR was used to non-specifically amplify viral DNA from fecal specimens. The amplified DNA was then cloned and sequenced for analysis. A novel virus was detected. Elucidation and analysis of the genome indicates it is a member of the Bocavirus genus of the Parvovirinae, 23% variant at the nucleotide level from its closest formally recognized relative, the Human Bocavirus (HBoV), and similar to the very recently proposed second species of Bocavirus (HBoV2). Fecal samples collected from case control pairs during 2001 for the AGE study were tested with a bocavirus-specific PCR, and HBoV2 (sequence confirmed) was detected in 32 of 186 cases with AGE (prevalence 17.2%) compared with only 15 controls (8.1%). In this same group of children, HBoV2 prevalence was exceeded only by rotavirus (39.2%) and astrovirus (21.5%) and was more prevalent than norovirus genogroup 2 (13.4%) and adenovirus (4.8%). In a univariate analysis of the matched pairs (McNemar's Test), the odds ratio for the association of AGE with HBoV2 infection was 2.6 (95% confidence interval 1.2-5.7); P = 0.007. During the course of this screening, a second novel bocavirus was detected which we have designated HBoV species 3 (HBoV3). The prevalence of HBoV3 was low (2.7%), and it was not associated with AGE. HBoV2 and HBoV3 are newly discovered bocaviruses, of which HBoV2 is the thirdmost-prevalent virus, after rotavirus and astrovirus, associated with pediatric AGE in this study.

Show MeSH
Related in: MedlinePlus