Panoramic Parvovirus Strain Discovery Data Chain

Download Strain's Sequence
Feedback for This Record
ParvoDB ID PV028163 GenBank Accession OP161116
Subfamily Parvovirinae Genus Dependoparvovirus
Species Dependoparvovirus primate1 Sequence Length 4600
Definition Adeno-associated virus 2 isolate JBL3, partial genome. Submission Date 2022-08-03
Strain Name JBL3 Sampling Date 2022
Sampling Country United Kingdom Location United Kingdom
Submitted By Roy,S., Williams,C.A., Bayzid,N., Bernal,L.M.M., Williams,R., Brown,J.R. and Breuer,J. Submitting Institution Infection Immunity and Inflammation, University College of London, 30 Guilford St, London, London WC1N 1EH, United Kingdom
Original Host Homo sapiens Sample Type Liver sample
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 RNAlater-ICE Used for infusion of frozen liver biopsies overnight before DNA/RNA purification. 36996872 View Related Publication
2 Qiagen AllPrep DNA/RNA Mini kit Used for DNA and RNA purification from liver biopsies.
3 Qiagen EZ1 Virus Mini kit Used for DNA and RNA purification from whole blood samples.
4 Feline calicivirus RNA Quality assurance control used during nucleic acid purification alongside clinical specimens to ensure quality.
5 Cowpox DNA Quality assurance control used during nucleic acid purification alongside clinical specimens to ensure quality.
6 MS2 phage RNA Internal control spiked into each sample during nucleic acid purification process.
7 KAPA RNA HyperPrep kit with RiboErase Used for rRNA depletion and library preparation of RNA from whole-blood samples with sufficient RNA yield.
8 NEBNext Microbiome DNA Enrichment Kit Used to deplete CpG-methylated DNA during DNA library preparation.
9 NEBNext Ultra II FS DNA Library Prep Kit Used for library preparation of DNA from whole blood samples and liver biopsies.
10 NextSeq High Output 150 cycle kit Sequencing reagent used for metagenomic sequencing of up to 12 libraries pooled per run.
11 MEGAHT-23TM Lubricating jelly Agent used during library preparation to ensure proper processing.
12 Porechop v0.2.4 Tool used to trim adapters during Nanopore sequencing data analysis.
13 SureSelectXT (Low Input and standard) Target Enrichment kits Used for hybridization capture probes for targeted enrichment sequencing.
14 AllType kits (VHBio/OneLambda) Used for high-resolution HLA typing method by next-generation sequencing.
15 Qubit fluorometer Quality control to quantify lysed proteins.
16 NanoDrop 2000 Used to quantify protein concentration from lysed tissue samples.
17 Femto Pulse System (Agilent) Used for high-resolution quality control to check DNA fragments size before sequencing.
18 PCR Used to confirm findings from metagenomic sequencing in blood and liver samples.
19 Turbo-DNA free kit (Thermo) Used for RNA samples to remove residual genomic DNA.
20 QuantiTect Reverse Transcription kit Used for reverse transcription of RNA samples to synthesize cDNA.
21 Qiagen Quantifast Fast mastermix Used in real-time PCR for targeting various gene sequences such as AAV2, HHV-6, and HAdV.
22 Optiview Detection Kit Used in conjunction with immunohistochemistry for detecting adenovirus.
23 Bond Polymer Refine Detection Kit Used in immunohistochemistry for detecting HHV-6, AAV2, and antibodies.
24 Diagenode Megaruptor 3 Used to fragment DNA to an average size of 10 kb for sequencing.
25 Leica Bond-III Used for immunohistochemistry staining in conjunction with various detection kits.