Panoramic Parvovirus Strain Discovery Data Chain

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ParvoDB ID PV019054 GenBank Accession JQ303061
Subfamily Parvovirinae Genus Bocaparvovirus
Species Bocaparvovirus primate2 Sequence Length 429
Definition Human bocavirus isolate PR5139/2009 non-structural protein 1 (NS1) gene, partial cds. Submission Date 2011-12-20
Strain Name PR5139/2009 Sampling Date 2009
Sampling Country Italy Location Italy
Submitted By Medici,M.C., Tummolo,F., Albonetti,V., Abelli,L.A., Chezzi,C. and Calderaro,A. Submitting Institution Department of Pathology and Laboratory Medicine, Section of Microbiology, University of Parma School of Medicine, Viale A. Gramsci, 14, Parma 43126, Italy
Original Host Homo sapiens Sample Type Faecal samples
Standardized Host Name Homo sapiens Host Tax Rank species
Standardized Host Class Mammalia Standardized Host Order Primates
Environmental Origin - N/A - Reagent Origin - N/A -
Number Reagent/Consumables Purpose PMID/Url Reference
1 Latex agglutination kits for group A RV and AdV (Orion Diagnostica, Espoo, Finland) Detection of group A rotavirus and adenovirus in stool samples. 22337304 View Related Publication
2 Reverse transcription-polymerase chain reaction (RT-PCR) kits (Nanogen Advanced Diagnostics, Turin, Italy) Detection of norovirus (NoV) in stool samples.
3 Balanced salt solution Storage solution for stool suspensions before further analysis.
4 EasyMAG (bioMerieux, Marcy l’Etoile, France) Automated extraction of nucleic acids from fecal suspensions.
5 Superscript One-Step RT-PCR for Long Templates (Invitrogen, Foster City, CA) One-step RT-PCR mix used in separate RT-PCRs for AstV and SaV.
6 Primers mon 269 and mon 270 Specific primers for the detection of astrovirus (AstV) in RT-PCR.
7 Primers by Okada et al. Specific primers for the detection of sapovirus (SaV) in RT-PCR.
8 AmpliTaq Gold DNA Polymerase with Gene Amp 10X PCR buffer (Applied Biosystems, Foster City, CA) PCR mix for the detection of bocavirus (BoV).
9 Primers Adel 1F and Adel 1R [Arthur et al., 2009] Specific primers for the detection of bocavirus (BoV) in PCR.
10 Ethidium bromide Staining agent for visualizing amplicons in agarose gel electrophoresis.
11 QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany) Purification of PCR amplicons for subsequent sequencing.
12 BigDye Terminator Cycle Sequencing Kit (Perkin Elmer–Applied Biosystem, Foster City, CA) Sequencing of purified PCR amplicons to identify and characterize viral strains.