Panoramic Parvovirus Strain Discovery Data Chain

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ParvoDB ID PV001219 GenBank Accession KR014422
Subfamily Parvovirinae Genus Bocaparvovirus
Species Bocaparvovirus primate1 Sequence Length 2016
Definition Human bocavirus 1 strain 642-Dec2009 VP1 (VP1) and VP2 (VP2) genes, complete cds. Submission Date 2015-03-19
Strain Name 642-Dec2009 Sampling Date 2009-12
Sampling Country Italy Location the emergency room of the Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, University of Milan, Italy
Submitted By Esposito,S., Zampiero,A., Piralla,A., Scala,A., Baldanti,F. and Principi,N. Submitting Institution Pediatric Clinic 1, Department of Pathophysiology and Transplantation, University of Milan and Fondazione IRCCS Ca Granda, Ospedale Maggiore Policlinico, via Commenda 9, Milano, MI 20122, Italy
Original Host Homo sapiens Sample Type nasopharyngeal swabs 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 paranasal flocked swab Collection of nasopharyngeal secretions from children 26267139 View Related Publication
2 universal transport medium (Kit Cat. No. 360c, Copan Italia, Brescia, Italy) Storage of nasopharyngeal swabs containing collected secretions
3 Nuclisens EasyMAG automated extraction system (Biomeriéux, Craponne, France) Extraction of viral nucleic acids from nasopharyngeal swabs
4 respiratory virus panel xTAG RVP FAST v2 (Luminex Molecular Diagnostics, Inc., Toronto, Canada) Simultaneous detection of various respiratory viruses, including hBoV, in extracted viral nucleic acids
5 TaqMan Universal Master Mix II (Applied Biosystems, California, USA) Reagent used for real-time PCRs to confirm hBoV presence
6 7900HT real-time PCR System machine (Applied Biosystems, California, USA) Amplification and detection of viral DNA in real-time PCR
7 NS-1 forward primer 5’-TGCAGACAACGCYTAGTTGTTT-3’ Primes the amplification of NS-1 target gene in real-time PCR
8 NS-1 reverse primer 5’-CTGTCCCGCCCAAGATACA-3’ Primes the amplification of NS-1 target gene in real-time PCR
9 NP-1 forward primer 5’-AGCATCGCTCCTACAAAAGAAAAG-3’ Primes the amplification of NP-1 target gene in real-time PCR
10 NP-1 reverse primer 5’-TCTTCATCACTTGGTCTGAGGTCT-3’ Primes the amplification of NP-1 target gene in real-time PCR
11 NS-1 probe 5’-CCAGGATTGGGTGGAACCTGCAAA-3’ Fluorescent probe for NS-1 target gene detection in real-time PCR
12 NP-1 probe 5’-AGGCTCGGGCTCATATCATCAGGAACA-3’ Fluorescent probe for NP-1 target gene detection in real-time PCR
13 Synthetic template control Positive control in PCR run
14 No-template control Negative control in PCR run
15 DNA plasmid Standard calibrator for obtaining viral load using real-time PCR
16 ND-1000 spectrophotometer (NanoDrop products, Wilmington, DE, USA) Detection of DNA plasmid concentrations
17 4 sets of primers for conventional PCR Primers used for amplifying viral VP-1/2 gene for genotyping
18 Quantitect Probe Master Mix (QIAGEN, Venlo, Netherlands) Reagent base for PCR amplification of VP-1/2 gene
19 QIAquick Gel Extraction Kit (QIAGEN, Venlo, Netherlands) Purification of PCR products from agarose gel
20 BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems, California, USA) Sequencing reactions for genotype analysis
21 3130 Genetic Analyser (Applied Biosystems, California, USA) Obtaining sequence data from sequencing reactions