Panoramic Parvovirus Strain Discovery Data Chain

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ParvoDB ID PV015731 GenBank Accession KF214639
Subfamily unclassified Parvoviridae Genus Parvo-like hybrid virus
Species NIH-CQV Sequence Length 3592
Definition Parvo-like hybrid virus UC10, partial genome. Submission Date 2013-06-08
Strain Name UC10 Sampling Date 2012-07-01
Sampling Country United States of America Location United States of America
Submitted By Naccache,S.N., Greninger,A.L., Delwart,E.L. and Chiu,C.Y. Submitting Institution Laboratory Medicine, University of California, San Francisco, 185 Berry Street, Box 0134, San Francisco, CA 94107, USA
Original Host Homo sapiens Sample Type clinical samples
Standardized Host Name Homo sapiens Host Tax Rank species
Standardized Host Class Mammalia Standardized Host Order Primates
Environmental Origin - N/A - Reagent Origin silica-binding spin columns used for nucleic acid extraction
Number Reagent/Consumables Purpose PMID/Url Reference
1 QIAamp UltraSens Virus Kit (Qiagen) Extract viral nucleic acid from serum samples in non-A-E hepatitis cohort 1. 24027301 View Related Publication
2 Illumina TruSeq Adapt DNA libraries constructed for sequencing.
3 0.22 μm filter (Millipore) Filter pooled serum samples to remove particles and debris.
4 QIAamp Viral RNA Mini Kit (Qiagen) Isolate viral nucleic acid that purifies both RNA and DNA.
5 EZ1 Viral Mini Kit v2.0 (Qiagen) Extract viral nucleic acids using an automated method.
6 epMotion 5075 BioRobot (Eppendorf) Prepare and automate library preparation.
7 ScriptSeq V2 RNA-Seq Kit (Epicentre) Construct sequencing libraries for deep sequencing.
8 Illumina MiSeq instrument Perform deep sequencing of the constructed libraries.
9 HIV-1 isolate DJ263 (CRF02_AG) Spike plasma samples for study.
10 BaseMatrix defibrinated human plasma (Seracare) Serve as negative plasma control.
11 RNeasy MinElute Cleanup Kit (Qiagen) Post-DNAse cleanup of viral nucleic acid.
12 TruSeq-adapted library Deep sequencing template for Illumina MiSeq instrument.
13 Agilent Bioanalyzer 2100 instrument (Agilent) Quantify NGS libraries prior to deep sequencing.
14 High Sensitivity DNA kit (Agilent) Evaluate DNA concentrations and quality.
15 KAPA Library Quantification Kit (Kapa Biosystems) Quantify the prepared sequencing libraries.
16 HotStarTaq DNA polymerase Kit (Qiagen) Conduct PCR screening for PHV.
17 lineacryl amide (Ambion) Replace carrier RNA during nucleic acid extractions.
18 RNeasy Mini Kit (Qiagen) Mock-extract nucleic acid with nuclease-free water for PCR screening.
19 QIAamp DSP Virus Kit (Qiagen) Verify PHV contamination potential in NA extraction.
20 PureLink Viral RNA/DNA Mini Kit (Invitrogen) Compare extraction methods with Qiagen columns.
21 TRIzol LS (Invitrogen) Alternate nucleic acid extraction method testing.
22 MagMax Viral RNA Isolation Kit (Ambion) Parallel re-extraction test for PHV from fecal and water samples.
23 Mock extractions using various water sources (Fisher, Qiagen, Epicentre) Examine the source of PHV contamination.