After collapsing in the late 1990s, the southern Gulf of St. Lawrence population of striped bass (Morone saxatilis) is recovering. Here, we evaluate the use of under-ice eDNA sampling to monitor the population and confirm overwintering locations. From 2018 to 2020, water samples were collected from transects spanning 35 km of the Miramichi River system, accounting for the effects of sampling site, month, sampling depth and tidal influence on eDNA concentration. We examined the distribution of eDNA in a complex tidal river system with a time series consisting of 12 h of continuous sampling throughout a tidal cycle, in conjunction with the use of artificial DNA tracers and acoustic Doppler current profiler flow measurements. The eDNA distribution correctly identified overwintering grounds based on acoustic tag data, including a perceptible upstream shift in 2020. Overall, there was no significant effect of year, sampling month (February or March), sampling depth or tidal phase on eDNA concentrations. The tidal time series revealed only weak patterns of eDNA recirculation. Monitoring eDNA concentration and distribution allows for a relative comparison of population size and location between years, and has the potential to be expanded to other river systems more easily than traditional acoustic fish tags and surveys.

The sole member of the Piscihepevirus genus (family Hepeviridae) is cutthroat trout virus (CTV) but recent metatranscriptomic studies have identified numerous fish hepevirus sequences including CTV-2. In the current study, viruses with sequences resembling both CTV and CTV-2 were isolated from salmonids in eastern and western Canada. Phylogenetic analysis of eight full genomes delineated the Canadian CTV isolates into two genotypes (CTV-1 and CTV-2) within the Piscihepevirus genus. Hepevirus genomes typically have three open reading frames but an ORF3 counterpart was not predicted in the Canadian CTV isolates. In vitro replication of a CTV-2 isolate produced cytopathic effects in the CHSE-214 cell line with similar amplification efficiency as CTV. Likewise, the morphology of the CTV-2 isolate resembled CTV, yet viral replication caused dilation of the endoplasmic reticulum lumen which was not previously observed. Controlled laboratory studies exposing sockeye (Oncorhynchus nerka), pink (O. gorbuscha), and chinook salmon (O. tshawytscha) to CTV-2 resulted in persistent infections without disease and mortality. Infected Atlantic salmon (Salmo salar) and chinook salmon served as hosts and potential reservoirs of CTV-2. The data presented herein provides the first in vitro and in vivo characterization of CTV-2 and reveals greater diversity of piscihepeviruses extending the known host range and geographic distribution of CTV viruses.