SPADA Meeting Book

vulnerable to “overfitting”: correctly differentiating known (i.e. sequenced) targets and non- 82 targets but failing to detect novel target variants or falsely detecting novel non-targets. 83 Knowledge of the true genetic diversity is limited for some biodefense agents and their near 84 neighbors, as often only several geographical and temporal representatives are fully 85 characterized while other geographic locations have been ignored or significantly under-sampled 86 and hence are under-represented. In addition, while some agents such as the bacterium Bacillus 87 anthracis are monomorphic (i.e. highly conserved), other agents, especially RNA viruses, are 88 very diverse (e.g., Lymphocytic choriomeningitis virus (LCMV), Lassa virus, and Crimean- 89 Congo hemorrhagic fever virus (CCHFV)). In general, detection assays targeting highly 90 conserved targets tend to fail due to unsequenced near-neighbor cross-reactivity, while assays 91 targeting diverse targets tend to fail due to false negatives against unsequenced target variants. 92 While the recent revolution in next generation sequencing technologies combined with 93 decreasing sequencing costs has increased knowledge of population genomic structure, the 94 capability for laboratory-based evaluation of newly sequenced strains has not kept pace. In this 95 scenario, replacing or redesigning older assays to incorporate new knowledge of the target 96 genomic landscape is critical. However, wet lab testing may not be feasible due to limitations on 97 the timely availability of samples/strains. This problem is further exacerbated by policy 98 decisions, such as the 2015 Department of Defense (DoD) moratorium that decreased access to 99 live/inactivated biodefense pathogens for various applications including assay development and 100 validation (1).

101 102

6