Experimental Design
Standard Operational Procedures (SOPs)
- SOP NGS Viruses
The aim of the protocol is to construct a viral enriched library for mass sequencing, using reclaimed water as a source of water, to detect viral pathogens.
- SOP ARB Samplings
This Standard Operation Procedure aims at the standardization of the consortium partners work within WP6. It should enable the partners to handle samples correctly and send the isolates to the LGL.
- SOP Intra FLA Metagenomics
The purpose of this procedure is to describe a method to analyze the 16S ribosomal RNA gene in order to study the biodiversity among the pathogenic bacteria from inside Free Living Amoeba (FLA) isolated from water.
- SOP MAF Filtration
The preparation protocol for Monolithic Adsorption Filtration (MAF) columns is based on the work of Peskoller et al. (Journal of Chromatography A, 2009). Adsorption of microorganisms and viruses to the MAF column is based on electrostatic interaction. Both microorganisms and viruses have a characteristic surface charge, which depends on the pH value of the surrounding matrix. The principle of the MAF process is to bind charged microorganisms and viruses to an oppositely charged MAF-Disk and afterwards elute them by change of the pH value with an elution buffer.
- SOP NA Extraction Qiagen
The aim of the protocol is to extract nucleic acids (NA) from irrigation water viral concentrates.
- SOP Protozoa Metagenomics
The purpose of this procedure is to describe a method to analyze the 18S ribosomal RNA gene in order to study the biodiversity among the protozoa present in water samples.
- SOP QPCR MST Indicators
This SOP describes the performance of specific qPCR for 6 DNA viruses (human adenovirus (HAdV), JC polyomavirus (JCPyV), porcine adenovirus (PAdV), bovine polyomavirus (BPyV), ovine polyomavirus (OPyV) and avian parvovirus (Ch/TyPV)) and 1 RNA virus used as process control, MS2 phage.
- SOP QPCR MST Standards
List of G-block gene fragments, as well as primers and probes for each specific PCR, nPCR and qPCR.
- SOP QPCR Virus
This SOP describes the procedure to implement specific qPCR for 6 DNA viruses (human adenovirus (HAdV), JC polyomavirus (JCPyV), porcine adenovirus (PAdV), bovine polyomavirus (BPyV), ovine polyomavirus (OPyV) and avian parvovirus (Ch/TyPV)) and 1 RNA virus used as process control, MS2 phage.
- SOP SM Floculation
The aim of the protocol is to concentrate viruses present in 10L of water into a final volume of 10mL (5mL in clean water to test higher volumes) of phosphate buffer.
