Fig. 1

PRV and IHNV challenge of Sockeye salmon. a A schematic diagram presents the experimental design of this study. Circles represent experimental tanks and roman numerals indicate the number of fish initially added to each respective tank. 1.) 900 Sockeye salmon representing 140 families were acclimated to 12 °C seawater. 2.) Fish were equally divided into three groups and administered 100 μL injections of either: media control (grey), media/blood homogenate control (blue), or media/blood homogenate containing PRV (orange). 3.) Tissue and blood samples were collected from three fish in each tank at 2, 5, 7, and 14 days post challenge. 4.) Immediately following 14d sampling, two tanks in each PRV challenge group were administered a 1 h immersion of either: media control (vertical lines) or media containing IHNV (checkerboard). 5.) Four hours following immersion, 28 fish from each tank were moved to a smaller corresponding tank. 6.) Tissue and blood samples were collected from four fish in each of the smaller tanks at 1, 3, 7, 21 and 34 days post immersion. Fish remaining in the larger tanks (n = 35/tank) were monitored for morbidity without sampling disturbance. (★) indicates the populations and relative timing for samples collected that were used in RNA-seq transcriptome profiling. b Data presents PRV L1 transcripts per μg total extracted RNA for head kidney and (c) blood samples collected from fish exposed to PRV by intraperitoneal injection. Samples from fish subsequently exposed to IHNV by immersion that did not develop detectable IHNV kidney infections (IHNV-) are also distinguished from samples with detectable IHN virus (IHNV+). d Presents IHNV N transcripts per μg total RNA for head kidney samples where IHNV was detectable by qPCR (n = 19 infected of 120 challenged). Samples from fish previously exposed and harboring PRV L1 transcripts are distinguished from mock injected controls. The number of PRV challenged IHNV exposed samples for which IHNV was not detected by qPCR is provided in brackets. e Kaplan-Meier survival curves of fish exposed to PRV, IHNV, or PRV and IHNV presented in 62 day time course in reference to PRV challenge (n = 105 per treatment group). In all instances, relative days post challenge to IHNV superinfection is also provided