Panoramic Parvovirus Strain Discovery Data Chain
| ParvoDB ID | PV014191 | GenBank Accession | OR542582 |
| Subfamily | Parvovirinae | Genus | Erythroparvovirus |
| Species | Erythroparvovirus primate1 | Sequence Length | 1122 |
| Definition | Human parvovirus B19 isolate MS-B19-17-25-839 VP1/2 structural protein gene, partial cds. | Submission Date | 2023-09-11 |
| Strain Name | MS-B19-17-25-839 | Sampling Date | 2017-05-09 |
| Sampling Country | Brazil | Location | Brazil |
| Submitted By | Lichs,G.G.C., Grillo,Z.C.F., Nascimento,V.A., Alcantara,D.M.C., Lemos,E.F., Carvalho,C.M.E., Demarchi,L.H.F., Goncalves,C.C.M., Naveca,F.G. and Favacho,A.R.M. | Submitting Institution | Biologia Molecular Lab, Foundation Oswaldo Cruz, Fiocruz Mato Grosso do Sul, Rua Gabriel Abrao, 92, Jardim das Nacoes, Campo Grande, Mato Grosso do Sul 79081-746, Brasil |
| Original Host | Homo sapiens | Sample Type | serum, urine, and cerebrospinal fluid 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 | QIAsymphony DSP Virus/Pathogen Mini Kit (QIAGEN) | Extraction of nucleic acids from each sample. | https://www.medrxiv.org/content/10.1101/2023.11.29.23299091v1 | View Related Publication |
| 2 | KAPA PROBE FAST qPCR Master Mix (2X) (Roche) | Performing real-time PCR (qPCR) for B19V detection. | ||
| 3 | ABI 7500 and QuantStudio 5 (Applied Biosystems) | Performing the real-time PCR (qPCR). | ||
| 4 | SuperFi II green enzyme (Thermo Fisher Scientific) | Performing PCR reactions for amplifying the viral genome. | ||
| 5 | GelRed (Biotium) | Staining agarose gel for visualizing DNA bands. | ||
| 6 | GeneRuler 1 kb DNA Ladder (Thermo Fisher Scientific) | Determining the size of PCR products. | ||
| 7 | Polyethylene glycol 8000 (Promega) | Precipitation of PCR products. | ||
| 8 | Microvolume spectrophotometer (Biodrop Duo Biochrom) | Quantification of DNA. | ||
| 9 | Qubit 2.0 and dsDNA HS Assay kit (Thermo Fisher Scientific) | Quantification of DNA for library preparation. | ||
| 10 | Nextera XT DNA Library Prep Kit (Illumina) | Library preparation for whole-genome sequencing. | ||
| 11 | MiSeq equipment and Reagent v2 500-cycle sequencing kit (Illumina) | Performing sequencing of DNA libraries. | ||
| 12 | Table S1 - Primers and probes | Specific oligonucleotides used for B19V detection via qPCR. | ||
| 13 | Table S2 - Reaction components and volumes | Specific reagents and volumes required for qPCR reactions. | ||
| 14 | Table S3 - Primers for amplification | Primers used to amplify the entire genome of B19V. |