Panoramic Parvovirus Strain Discovery Data Chain
| ParvoDB ID | PV015797 | GenBank Accession | OQ835745 |
| Subfamily | Densovirinae | Genus | unclassified Densovirinae |
| Species | Densovirinae sp. | Sequence Length | 6520 |
| Definition | Densovirinae sp. strain Cameroon/U172329/2017, complete genome. | Submission Date | 2023-04-17 |
| Strain Name | Cameroon/U172329/2017 | Sampling Date | 2017 |
| Sampling Country | Cameroon | Location | Cameroon |
| Submitted By | Orf,G.S., Olivo,A., Harris,B., Weiss,S.L., Achari,A., Yu,G., Federman,S., Mbanya,D., James,L., Mampunza,S., Chiu,C.Y., Rodgers,M.A., Cloherty,G.A. and Berg,M.G. | Submitting Institution | Infectious Disease Research, Abbott Diagnostics, 100 Abbott Park Rd, Abbott Park, IL 60064, USA |
| Original Host | Homo sapiens | Sample Type | Clinical specimens of whole blood and plasma |
| 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 | EZ1 Virus Mini Kit | To extract total nucleic acid from plasma samples. | 37113001 | View Related Publication |
| 2 | Turbo DNase | To treat extracted nucleic acid to remove DNA. | ||
| 3 | RNA Clean & Concentrator Kit | To purify treated nucleic acid and elute in water. | ||
| 4 | Benzonase | To treat plasma samples before nucleic acid extraction. | ||
| 5 | m2000sp workstation (Abbott Molecular) | To extract total nucleic acids with a research-use only RNA/DNA protocol. | ||
| 6 | qScript XLT cDNA SuperMix kit | To convert RNA into cDNA. | ||
| 7 | Nextera XT library prep kit | For sequencing library construction. | ||
| 8 | AMPure XP magnetic purification beads (Beckman Coulter) | To purify prepared libraries and elute in resuspension buffer. | ||
| 9 | SuperScript III first-strand system | For first-strand synthesis during cDNA preparation. | ||
| 10 | Sequenase v2.0 polymerase | For second-strand synthesis during cDNA preparation. | ||
| 11 | TapeStation 2200 Bioanalyzer (Agilent Technologies) | To assess the size of NGS libraries. | ||
| 12 | Qubit 2.0 Fluorometer (ThermoFisher) | To assess the concentration of NGS libraries. | ||
| 13 | Quantum dx qScript XLT cDNA Kit (Quantabio) | To convert RNA into cDNA for NGS library preparation. | ||
| 14 | illuminated dual-index primers (Integrated DNA Technologies) | For barcoding Nextera XT libraries. | ||
| 15 | Resuspension buffer (Illumina) | For purifying and eluting NGS libraries. | ||
| 16 | SPADES | For de novo assembly of viral genomes. | ||
| 17 | random hexamers (catalog number N8080127, Thermo-Fisher Scientific) | For unbiased cDNA synthesis in MSSPE. |