SmartScreen-AIS: A High-Throughput qPCR Chip for Nationwide Surveillance of Aquatic Invasive Species

Effective wildlife conservation requires frequent and widespread data on species occurrence. With the maturation of eDNA-based monitoring—now widely recognized as sensitive, cost effective, and legally defensible—nationally coordinated eDNA strategies are beginning to take shape. Such ambitious initiatives will require eDNA analytics with the throughput and sensitivity required for surveillance of many protected, pathogenic, and invasive species across broad geographic scales. Here, we help meet this need with SmartScreen-AIS: a high-throughput qPCR (HT-qPCR) chip with 46 assays targeting aquatic invasive species of widespread concern. SmartScreen-AIS was validated for use throughout the continental United States and can be subdivided into smaller chip formats as desired for use in specific regions or biomes. Assay performance in HT-qPCR was strong relative to conventional qPCR, with slightly lower specificity in some cases (due to pre-amplification) but significantly higher sensitivity. Contamination was rare, PCR inhibition was minimal to nonexistent, and demonstration at three military installations detected eDNA from all species on the chip that were known to be present and one species that was previously undocumented. Cost savings will depend on the number of assays used and samples tested, but in this study we estimate that eDNA analyses were 75% cheaper using HT-qPCR than they would be with our conventional qPCR protocol. To facilitate use, we provide appendices with assay details, bench protocols, a script for processing results, and an online app with state-level assay specificity information. SmartScreen-AIS has the potential to advance early detection of invasive species in the United States, and we hope our HT-qPCR workflow inspires chip development and use globally.