Comprehensive pathogen diagnostics in wild fish populations using blood-based molecular strategies: an Atlantic herring case study

TL;DR

This study uses blood-based molecular methods to detect pathogens in Atlantic herring, revealing the prevalence and activity of two key threats in wild fish populations.

Contribution

The study introduces a combined PCR and RNA-Seq approach using FTA cards for pathogen diagnostics in wild fish.

Findings

33% of Atlantic herring tested positive for erythrocytic necrosis virus (ENV) and 10% for Ichthyophonus.

ENV was more common in estuarine and coastal areas, showing a clustered spatial distribution.

RNA-Seq detected active ENV replication but no major host transcriptional response in infected fish.

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.

The online version contains supplementary material available at 10.1038/s41598-025-28653-8.

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