Panoramic Parvovirus Strain Discovery Data Chain

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ParvoDB ID PV007916 GenBank Accession LC772179
Subfamily Parvovirinae Genus Protoparvovirus
Species Protoparvovirus primate3 Sequence Length 1060
Definition Cutavirus JPN-PP3 genes for VP1, VP2, partial cds. Submission Date 2023-06-23
Strain Name JPN-PP3 Sampling Date 2011
Sampling Country Japan Location Japan
Submitted By Hashida,Y. and Daibata,M. Submitting Institution Contact:Yumiko Hashida Kochi medical school, Kochi university, Department of microbiology and infection; Kohasu Oko-cho, Nankoku, Kochi 783-8505, Japan
Original Host Homo sapiens Sample Type skin 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 Formalin-fixed, paraffin-embedded (FFPE) biopsy specimens Specimens from lesional skin stored for evaluation of CuV status 37995315 View Related Publication
2 Sterile cotton swabs moistened with phosphate-buffered saline Collection of skin swabs from lesional and healthy skin
3 TaqMan-based real-time quantitative polymerase chain reaction (qPCR) Detection and quantification of CuV DNA
4 Primers and probes (targeting VP1 and VP2 genes) Amplification of CuV VP1 and VP2 genes
5 Microtome blades Slicing FFPE blocks to prevent cross-contamination
6 Molecular biology-grade water No-template controls in PCR assays
7 RNAscope 2.5 HD Reagent Kit-Brown Colorimetric RNA ISH for CuV RNA detection
8 V-CuV-VP1-VP2-C1 probes Targeting CuV NS1, middle ORF, and VP1/VP2 genes in RNA ISH
9 Probes targeting human PPIB and bacterial DapB Positive and negative ISH technical controls
10 Antibodies against human CD3, CD4, and CD20 (Nichirei Bioscience) Immunohistochemistry to identify infiltrating immune cells
11 RNeasy FFPE kit (QIAGEN) Extraction of total RNA from biopsies
12 DNase Prevention of viral DNA amplification during RNA extraction
13 SuperScript IV VILO Master Mix with ezDNase Enzyme (Thermo Fisher Scientific) Reverse transcription of RNA to cDNA
14 Primers for CuV genes PCR amplification of CuV gene segments
15 PCR products Purification and sequencing for CuV sequence analysis
16 DNA sequencing Determining the sequence of CuV genome fragments