Abstract
Climate change affects marine ecosystems by promoting pathogens that threaten key fish populations. To protect these, monitoring programs must adapt to manage threats and sustain fisheries. Here, we combined traditional PCR methods and transcriptomic analysis from a single drop of blood stored on FTA cards to determine the prevalence of erythrocytic necrosis virus (ENV) and the Ichthyophonus parasite in the Atlantic herring population. Across 2023–2024, 33% of individual blood samples tested positive for ENV and 10% for Ichthyophonus by PCR, with ENV-positive fish more frequently found in estuarine and coastal areas. Spatial analyses revealed a clustered distribution for ENV and a more sporadic occurrence of Ichthyophonus. RNA-Seq detected viral RNA fragments in ENV PCR-positive fish, revealing high levels of viral transcripts consistent with active viral replication. However, no significant changes were observed in the host blood transcriptome between infected and uninfected individuals, suggesting that ENV replication may proceed with limited systemic host transcriptional response under subclinical conditions. Overall, our study provides the first comprehensive baseline on the prevalence and molecular activity of ENV and Ichthyophonus in Atlantic herring, demonstrating the power of FTA-based RNA-Seq diagnostics to uncover hidden infections and informing future surveillance and management of wild fish populations.
Data availability
The raw sequencing data for the transcriptomic analyses generated in this study have been deposited in the NCBI Sequence Read Archive (SRA) under accession number PRJNA1258723. All other relevant data supporting the findings of this study are available within the article and its Supplementary Information files.
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Acknowledgements
This research was performed with the logistical support of Fisheries and Oceans Canada (DFO). The authors would like to thank all the DFO personnel, particularly Jacob Burbank and Laurie Maynard, for their assistance and hospitality during the survey of the Southern Gulf of St. Lawrence. They would also like to thank Marlène Fortier for her excellent technical help.
Funding
This work was funded by the Fonds de Recherche du Québec-Nature et Technologie (Y.S.P. and D. R.) and the National Science and Engineering Research Council of Canada (Grant No. x-2019-06607, YSP). F.F. is supported by a scholarship from the Fonds de Recherche du Québec-Nature et Technologie (FRQNT). D.R. is supported by the Canada Research Chair Program. This work was supported by CFI-MSI GlycoNet Integrated Services (GIS-11, Y.S.P).
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DR, FC, FF, and YSP conceived the study. All authors were responsible for the interpretation of data and critical appraisal. All authors executed the experiments and contributed to the experimental design and analyses of the results. FC and YSP drafted the manuscript with input from all authors.
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Caza, F., Fronton, F., Ennia, L. et al. Comprehensive pathogen diagnostics in wild fish populations using blood-based molecular strategies: an Atlantic herring case study.
Sci Rep (2025). https://doi.org/10.1038/s41598-025-28653-8
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DOI: https://doi.org/10.1038/s41598-025-28653-8
Keywords
- Atlantic herring
- Pathogens
Ichthyophonus
- Erythrocytic necrosis virus
- Transcriptomics
- FTA cards
Source: Ecology - nature.com
