Panoramic Parvovirus Strain Discovery Data Chain

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ParvoDB ID PV016644 GenBank Accession KX035107
Subfamily Densovirinae Genus Iteradensovirus
Species Iteradensovirus incertum2 Sequence Length 4678
Definition Human CSF-associated densovirus putative nonstructural protein NS1, nonstructural protein NS2, nonstructural protein NS3, and structural protein VP genes, complete cds. Submission Date 2016-04-07
Strain Name 21 Sampling Date 2013
Sampling Country United States of America Location Colorado, United States of America
Submitted By Phan,T. and Delwart,E. Submitting Institution Virology, Blood Systems Research Institute, 270 Masonic Avenue, San Francisco, CA 94118, USA
Original Host Homo sapiens Sample Type CSF specimens
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 CSF specimens Collected from patients with encephalitis without identified infectious etiology for analysis. 27522586 View Related Publication
2 0.45-μm filter (Millipore) To filter CSF specimen pools after centrifugation.
3 Nuclease enzymes To digest unprotected nucleic acids in the filtered CSF samples.
4 Maxwell 16 automated extractor (Promega) To extract viral nucleic acids from the treated samples.
5 Random RT-PCR To generate cDNA and DNA from extracted viral nucleic acids.
6 Nextera XT Sample Preparation Kit (Illumina) To construct a DNA library for deep sequencing.
7 Primers Huca-F1 (5′-CTG GAA GCG ACG AAG ATG GAC T-3′) and Huca-R1 (5′-CTT TGT CCA TCT CCT CTG CGG TG-3′) For the first round of PCR to identify the specimen containing densovirus DNA.
8 Primers Huca-F2 (5′-ACT ATG CTC TCC CTT TCC GAC-3′) and Huca-R2 (5′-CAT ACT TGT CTC CAG GAA TCT TGT C-3′) For the second round of PCR to identify the specimen containing densovirus DNA.