Panoramic Parvovirus Strain Discovery Data Chain

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ParvoDB ID PV013379 GenBank Accession MK387160
Subfamily Parvovirinae Genus Bocaparvovirus
Species Bocaparvovirus primate1 Sequence Length 547
Definition Human bocavirus 1 isolate SA-MKH-5760 structural protein VP1 gene, partial cds. Submission Date 2019-01-09
Strain Name SA-MKH-5760 Sampling Date from 2009-04 to 2015-04
Sampling Country South Africa Location South Africa
Submitted By Netshikweta,R., Chidamba,L., Nadan,S., Page,N. and Taylor,M. Submitting Institution Plant and Soil Sciences, University of Pretoria, Lunnon RD Hatfield campus, Pretoria, Gauteng 0002, South Africa
Original Host Homo sapiens Sample Type stool 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 QIAamp Viral RNA Mini Kit To extract viral nucleic acid (both DNA and RNA) from the fecal suspensions. 31755120 View Related Publication
2 Eppendorf centrifuge 5430 To clarify fecal suspensions by centrifugation at 5000g for 5 minutes.
3 QIAcube extractor (Qiagen) To perform automatic extraction of viral nucleic acid as part of the protocol specified in the QIAamp Viral RNA Mini Kit.
4 Buffer To elute the extracted viral nucleic acid after processing in the QIAcube extractor.
5 Real-time polymerase chain reaction (PCR) reagents To screen all specimens for Human bocavirus (HBoV) by targeting the highly conserved NS1 region.
6 Enzyme immunoassays To test for the presence of Rotavirus (RV) in stool specimens.
7 Reverse transcription (RT)-PCR To test for Rotavirus (RV), and to perform conventional and real-time RT-PCR detection of other viruses like Norovirus (NoV), Sapovirus (SaV), and human Astrovirus (AstV).
8 DNA Baser Sequence Assembler v5.15 (Heracle BioSoft SRL) To assemble the forward and reverse sequences before confirming sequence identity with a BLAST search.
9 QIAquick PCR purification kit (Qiagen) For purification of PCR amplicons before sequencing.
10 ExoSAP-IT (USB Corporation) To purify PCR products before sequencing.
11 ABI 3500 Genetic Analyzer (Applied Biosystems/Life Technologies) To sequence the purified PCR products.
12 AmpliPrep automated extraction (Roche Diagnostics GmbH, Mannheim, Germany) To test dried blood spots for HIV RNA along with COBAS TaqMan automated real-time detection.