Panoramic Parvovirus Strain Discovery Data Chain

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ParvoDB ID PV020706 GenBank Accession MT410190
Subfamily Parvovirinae Genus Erythroparvovirus
Species Erythroparvovirus primate1 Sequence Length 5590
Definition Human parvovirus B19 isolate AA-07 nonstructural protein (NS1) and capsid protein 1 (VP1) genes, complete cds. Submission Date 2020-04-27
Strain Name AA-07 Sampling Date 2015
Sampling Country Finland Location Finland
Submitted By Toppinen,M., Pratas,D., Hedman,K., Perdomo,M.F. and Sajantila,A. Submitting Institution Virology, University of Helsinki, Haartmaninkatu 3, Helsinki 00290, Finland
Original Host Homo sapiens Sample Type bone
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 Oscillating tip saw Cutting femoral diaphysis longitudinally 32668397 View Related Publication
2 Toothbrush Cleaning bone
3 Distilled water Washing bone
4 0.1 % sodium hypochlorite Disinfecting bone during washing
5 96.1 w/w ethanol Sterilizing bone during washing
6 Dentist drill (Schick Qube) Sampling external and internal surfaces of femoral bone
7 Spex 6775 Freezer/mill Cryomilling bone
8 Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific) Quantitating total DNA
9 Genomic DNA Reagent Kit (Perkin Elmer) Evaluating quality of total DNA
10 Commercial qPCR kits (Hepatitis B Virus PCR Kit, GeneProof; Genesig Human papillomavirus 31 Standard kit, PrimerDesign) Quantifying hepatitis B virus and human papillomavirus type 31 DNA
11 Maxima probe qPCR Master mix (Thermo Fisher Scientific) qPCR reactions
12 ROX passive reference dye Reference dye in qPCR
13 EDTA Used in lysis buffer to evaluate PCR inhibition due to residual EDTA
14 MgCl2 Examining the impact of residual Ca2+-ions on qPCR performance
15 KAPA HyperPlus library preparation kit (Roche) Preparing sequencing libraries
16 Covaris E220 Mechanical fragmentation of DNA
17 xGen Dual Index UMI Adapters (Integrated DNA Technologies) Adapters used during library preparation
18 DNA High Sensitivity Reagent Kit (LabChip GX Instrument, Perkin Elmer) Analyzing fragment length distributions after sonication
19 MyBaits v4 kit (Arbor Biosciences) Performing viral enrichment via RNA baits
20 xGen Universal Blockers-TS Mix (Integrated DNA Technologies) Blocking unspecific binding during hybridization in viral enrichment
21 KAPA Pure Beads (Roche) Performing clean-up steps during library preparation and viral enrichment
22 MinElute PCR Purification Kit (Qiagen) Clean-up during library prep and enrichment
23 KAPA Library Quantification Kit (Roche) Quantifying enriched libraries
24 Statagene 3005P qPCR System (Agilent) Quantitative PCR analysis
25 NovaSeq 6000 SP PE151 reagent kit (Illumina) Sequencing pooled enriched libraries