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APPLICATION OF VIRULENCE FACTOR ACTIVITY RELATIONSHIPS (VFAR) TO VIRUSES ISOLATED FROM SOURCE AND DRINKING WATER
Impact/Purpose:
Overarching Objectives and Links to Multi-Year Planning
This task directly supports the 2003 Drinking Water Research Program Multi-Year Plan's long term goal 2 to "develop new data, innovative tools and improved technologies to support decision making by the Office of Water on the Contaminate Candidate List and other regulatory issues, and implementation of rules by states, local authorities and water utilities" under GRPA Goal 2 (Clean and Safe Water). The overarching objective is to provide the Office of Water, Agency risk assessors and managers, scientists, state regulators, water industry and industry spokes groups with an evaluation of the use of the VFAR approach for determining which human enteric viruses should be on future CCL lists.
Specific Subtask Objectives:
o Conduct a bioinformatics study of human caliciviruses to determine appropriate regions to target for VFAR studies (to be completed by 9/05 in support of Long Term Goal 2 (due 2010)).
o Develop a microarray assay for typing human caliciviruses (to be completed by 9/06 in support of Long Term Goal 2 (due 2010)).
Description:
EPA is required to publish a new Contaminant Candidate List (CCL) every five years. The CCL is to contain chemical and microbial contaminants known or anticipated to occur in public water supplies. In a review of the process used by EPA to choose contaminants for new CCLs, the National Research Council (NRC) recommended that EPA use molecular genomics and bioinformatics to determine Virulence Factor Activity Relationships (VFAR) among possible microbial candidates. The theoretical VFAR approach for microbial agents is based upon the successful use of structure-activity relationships to predict toxicity and other properties of new chemicals. The NRC proposed this approach because it was recognized that the identification of contaminants based on traditional approaches will likely slow identification of agents causing waterborne disease and underestimate the level of exposure to these agents from drinking water. The application of new time-saving genomic or proteomic techniques may help address this shortcoming. Under the VFAR approach, virulence factors detected by these new techniques might identify pathogenic agents in water that have not yet been linked to waterborne outbreaks.
The use of the VFAR approach as defined in the NRC report is generally less complex for viruses than for bacterial or protozoan pathogens. Viruses do have specific genes that directly affect virulence (e.g., capsid genes that provide receptors to specific target organs) and comparison of viral genomes found in waters with the genomes of known pathogens is possible using PCR and sequence data or microarray analysis as the NRC report suggests. The approach is feasible because the type strains of many viral pathogens have been sequenced.
This task is an evaluation of the VFAR approach using noroviruses initially and then other emerging viruses, such as hepatitis E virus. Noroviruses are the group of human caliciviruses that have caused many waterborne outbreaks. They are grouped into two major genogroups with a number of subtypes in each genogroup. Subtypes differ in their virulence properties, and genogroup II, subtype 4 strains have been reported to cause the more virulent outbreaks occurring worldwide during 2002-3. In this task, the genome regions that allow the grouping of waterborne viruses into subtypes will be identified. A microarray assay will be developed from these regions and, when necessary, microarray data will be supplemented by DNA sequencing. The data obtained from these assays will be compared with virulence data as it becomes available.