Summary
Detection of human pathogenic viruses in produce or irrigation water currently relies on culture- based methods of bacterial indicators, which frequently fail to correlate with the presence of enteric viruses. Culture-independent metagenomic approaches (i.e. massive sequencing) provide the highest resolution to analyze species diversity and will be applied to irrigation water, stools (which may contaminate agricultural and produce handling facilities by food handlers) and produce in order to search for new indicators. Our project goal is to identify viral specie/s which correlates with presence/abundance of pathogenic viruses in irrigation waters and produce.
Our specific objectives are:
1) Optimization of sample preparation procedure for viral metagenomics from irrigation water samples
2) Determination of the viral community composition of samples previously analyzed that tested positive or negative for the presence of human pathogenic viruses
3) Identification of specific viral species or groups whose presence/abundance correlates with the occurrence of human pathogenic viruses in stools, irrigation waters and produce. The identification of meaningful viral indicator/s will allow produce industry to simplify the control of enteric viruses by an easy and rapid procedure to detect and quantify the indicator, which in a short term will be implemented in the produce chain.
