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Calicivirus from novel Recovirus genogroup in human diarrhea, Bangladesh.

Smits SL, Rahman M, Schapendonk CM, van Leeuwen M, Faruque AS, Haagmans BL, Endtz HP, Osterhaus AD - Emerging Infect. Dis. (2012)

Bottom Line: To identify unknown human viruses in the enteric tract, we examined 105 stool specimens from patients with diarrhea in Bangladesh.A novel calicivirus was identified in a sample from 1 patient and subsequently found in samples from 5 other patients.Phylogenetic analyses classified this virus within the proposed genus Recovirus.

View Article: PubMed Central - PubMed

Affiliation: Erasmus Medical Center, Rotterdam, the Netherlands. smits@viroclinics.com

ABSTRACT
To identify unknown human viruses in the enteric tract, we examined 105 stool specimens from patients with diarrhea in Bangladesh. A novel calicivirus was identified in a sample from 1 patient and subsequently found in samples from 5 other patients. Phylogenetic analyses classified this virus within the proposed genus Recovirus.

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Schematic outline of the strategies used for PCR amplification of calicivirus Bangladesh/289/2007. A) Schematic representation of the calicivirus Bangladesh/289/2007 genome. Boxes represent the open reading frames encoding the calicivirus proteins. Indicated are the poly(A)-tail (An); putative cleavage sites indicated by XX↓XX. The 5′ end of the genome was not obtained. The bottom of the panel shows a schematic outline of the reverse transcription PCRs employed to amplify calicivirus Bangladesh/289/2007 sequences by using random amplification, degenerate PCR, and 3′ rapid amplification of cDNA ends (RACE) PCR. The orientations and positions of the oligonucleotides on the calicivirus genome are depicted and sequences shown in Technical Appendix Table 2. B) Genome organization of caliciviruses in the genera Vesivirus, Nebovirus, Norovirus, Sapovirus, and Lagovirus and proposed genera Valovirus and Recovirus, for comparison with the new calicivirus Bangladesh/289/2007. The 5′ end of the genome is shown with a Vpg protein (black dots). Numbers indicate the nucleotide positions according to the virus genome for which the GenBank accession number is indicated.
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Figure 1: Schematic outline of the strategies used for PCR amplification of calicivirus Bangladesh/289/2007. A) Schematic representation of the calicivirus Bangladesh/289/2007 genome. Boxes represent the open reading frames encoding the calicivirus proteins. Indicated are the poly(A)-tail (An); putative cleavage sites indicated by XX↓XX. The 5′ end of the genome was not obtained. The bottom of the panel shows a schematic outline of the reverse transcription PCRs employed to amplify calicivirus Bangladesh/289/2007 sequences by using random amplification, degenerate PCR, and 3′ rapid amplification of cDNA ends (RACE) PCR. The orientations and positions of the oligonucleotides on the calicivirus genome are depicted and sequences shown in Technical Appendix Table 2. B) Genome organization of caliciviruses in the genera Vesivirus, Nebovirus, Norovirus, Sapovirus, and Lagovirus and proposed genera Valovirus and Recovirus, for comparison with the new calicivirus Bangladesh/289/2007. The 5′ end of the genome is shown with a Vpg protein (black dots). Numbers indicate the nucleotide positions according to the virus genome for which the GenBank accession number is indicated.

Mentions: One sample, no. 289, yielded a novel mammalian virus from the family Caliciviridae that we further characterized by near full-length genome sequencing using random amplification with next-generation sequencing, specific reverse transcription PCRs, and 3′ rapid amplification of cDNA ends PCR (Figure 1, panel A) as described (6,7). We named the virus isolate calicivirus Bangladesh/289/2007 (GenBank accession no. JQ745645).


Calicivirus from novel Recovirus genogroup in human diarrhea, Bangladesh.

Smits SL, Rahman M, Schapendonk CM, van Leeuwen M, Faruque AS, Haagmans BL, Endtz HP, Osterhaus AD - Emerging Infect. Dis. (2012)

Schematic outline of the strategies used for PCR amplification of calicivirus Bangladesh/289/2007. A) Schematic representation of the calicivirus Bangladesh/289/2007 genome. Boxes represent the open reading frames encoding the calicivirus proteins. Indicated are the poly(A)-tail (An); putative cleavage sites indicated by XX↓XX. The 5′ end of the genome was not obtained. The bottom of the panel shows a schematic outline of the reverse transcription PCRs employed to amplify calicivirus Bangladesh/289/2007 sequences by using random amplification, degenerate PCR, and 3′ rapid amplification of cDNA ends (RACE) PCR. The orientations and positions of the oligonucleotides on the calicivirus genome are depicted and sequences shown in Technical Appendix Table 2. B) Genome organization of caliciviruses in the genera Vesivirus, Nebovirus, Norovirus, Sapovirus, and Lagovirus and proposed genera Valovirus and Recovirus, for comparison with the new calicivirus Bangladesh/289/2007. The 5′ end of the genome is shown with a Vpg protein (black dots). Numbers indicate the nucleotide positions according to the virus genome for which the GenBank accession number is indicated.
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Related In: Results  -  Collection

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Figure 1: Schematic outline of the strategies used for PCR amplification of calicivirus Bangladesh/289/2007. A) Schematic representation of the calicivirus Bangladesh/289/2007 genome. Boxes represent the open reading frames encoding the calicivirus proteins. Indicated are the poly(A)-tail (An); putative cleavage sites indicated by XX↓XX. The 5′ end of the genome was not obtained. The bottom of the panel shows a schematic outline of the reverse transcription PCRs employed to amplify calicivirus Bangladesh/289/2007 sequences by using random amplification, degenerate PCR, and 3′ rapid amplification of cDNA ends (RACE) PCR. The orientations and positions of the oligonucleotides on the calicivirus genome are depicted and sequences shown in Technical Appendix Table 2. B) Genome organization of caliciviruses in the genera Vesivirus, Nebovirus, Norovirus, Sapovirus, and Lagovirus and proposed genera Valovirus and Recovirus, for comparison with the new calicivirus Bangladesh/289/2007. The 5′ end of the genome is shown with a Vpg protein (black dots). Numbers indicate the nucleotide positions according to the virus genome for which the GenBank accession number is indicated.
Mentions: One sample, no. 289, yielded a novel mammalian virus from the family Caliciviridae that we further characterized by near full-length genome sequencing using random amplification with next-generation sequencing, specific reverse transcription PCRs, and 3′ rapid amplification of cDNA ends PCR (Figure 1, panel A) as described (6,7). We named the virus isolate calicivirus Bangladesh/289/2007 (GenBank accession no. JQ745645).

Bottom Line: To identify unknown human viruses in the enteric tract, we examined 105 stool specimens from patients with diarrhea in Bangladesh.A novel calicivirus was identified in a sample from 1 patient and subsequently found in samples from 5 other patients.Phylogenetic analyses classified this virus within the proposed genus Recovirus.

View Article: PubMed Central - PubMed

Affiliation: Erasmus Medical Center, Rotterdam, the Netherlands. smits@viroclinics.com

ABSTRACT
To identify unknown human viruses in the enteric tract, we examined 105 stool specimens from patients with diarrhea in Bangladesh. A novel calicivirus was identified in a sample from 1 patient and subsequently found in samples from 5 other patients. Phylogenetic analyses classified this virus within the proposed genus Recovirus.

Show MeSH
Related in: MedlinePlus