Passive eDNA sampling to monitor infectious hypodermal and haematopoietic necrosis virus (IHHNV) in pond-reared giant black tiger shrimp (Penaeus monodon) aquaculture systems

Passive sampling of environmental nucleic acids (eDNA and eRNA) has potential as a simple, effective, and cost-efficient method for pathogen surveillance in aquaculture. This study evaluated passive eDNA sampling for targeted detection and quantification of infectious hypodermal and haematopoietic necrosis virus (IHHNV) in giant black tiger shrimp, Penaeus monodon, aquaculture ponds. The ability of eDNA to estimate IHHNV host infection was evaluated through two investigations, comparing TaqMan qPCR detections of IHHNV from passively sampled eDNA and shrimp tissue samples from the same ponds. Passive sampling of eDNA involved timed submersion of membrane filters, within protective housings, in shrimp ponds. The effect of submersion duration on IHHNV detection was initially evaluated by submerging passive samplers for 1, 2, 4, 6 and 24 h across five ponds at 159-169 days of shrimp culture (DOC). Longer passive sampler submersion durations increased IHHNV detection from eDNA, and IHHNV loads were strongly correlated between eDNA and shrimp tissue. Passive eDNA samplers were then deployed at a farm-scale in 22 earthen shrimp ponds (125-129 DOC) for 24 h, given the higher IHHNV detection at 24 h in the initial study. The farm-scale deployment showed 95 % agreement in identifying ponds as IHHNV positive using eDNA and shrimp samples. Mean IHHNV loads in ponds were strongly correlated between eDNA and shrimp tissue ( R 2 = 0.95), indicating the potential of eDNA detection to approximate host infection levels. These findings provide evidence to advance the use of passive eDNA sampling for accurate and efficient monitoring of IHHNV in shrimp aquaculture systems. • Passive sampling captures nucleic acids on filters during environmental incubation • Passive sampling was evaluated for quantifying IHHNV eDNA in shrimp ponds • IHHNV was detected by qPCR from eDNA after 1, 2, 4, 6 and 24 h of incubation • IHHNV loads were highly correlated between pond eDNA and shrimp tissues • eDNA has high potential for estimating shrimp host infection levels