SPADA Draft Documents

Assay Stewardship – when new virus or bacterial strains are discovered, will the existing assay 688 work? 689 After an assay is designed and validated, it is relatively common for the scientific community 690 to discover a new strain of a pathogen that has a new mutation at a site that causes the assay to 691 fail for that new isolate. This is termed “signature erosion” (9). To date, there have not been any 692 good methods for anticipating new mutations. One general recommendation is to design primers 693 to be a little longer than needed for a perfect match so that in the event that a single or double 694 mutation occurs at a later time, then the primer will still work as long as the new mutation does 695 not occur at the 3’-end of either primer. In addition, there is a need to have software that can take 696 existing validated assays and computationally test new sequenced isolates to predict if the new 697 isolate is likely to be “covered” by the existing assay (i.e. the existing assay is predicted to give 698 an amplicon for the new isolate with high efficiency), or if the existing assay is likely to fail for 699 the new isolate (i.e. the existing assay is predicted to give an amplicon for the new isolate with 700 low efficiency). Even better would be for software to constantly monitor existing databases for 701 new entries and to automatically alert a user or agency if a new isolate is “high risk” for assay 702 failure. Such a capability would allow for real-time monitoring of assays to alert agencies in 703 charge of protecting the public with a mechanism to focus their ongoing validation efforts on 704 those assays that have a high likelihood of failure rather than wasting resources on unnecessary 705 redundant validations. Funding, development, and implementation of such an assay stewardship 706 approach is highly recommended by the SPADA working group.

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