Biosecurity and Vaccines for Emerging Aquatic Animal RNA Viruses

Abstract

Emerging RNA viruses pose a critical threat to aquatic animals, leading to significant ecological and economic consequences. Their high mutation rates and genetic adaptability drive rapid evolution, cross-species transmission, and expanding host ranges, complicating disease management. In aquaculture, RNA viruses are responsible for major outbreaks in fish, while DNA viruses predominate in crustaceans. Marine mammals are increasingly affected by morbilliviruses and highly pathogenic avian influenza (HPAI) H5N1, which has caused widespread mortality events in pinniped and cetacean populations, raising concerns about zoonotic spillover. The absence of effective antiviral treatments and the complexity of vaccine development highlight the urgent need for enhanced biosecurity measures. Furthermore, novel vaccine approaches, such as self-assembling protein nanocage platforms, offer promising solutions for RNA virus mitigation. This review provides a comprehensive analysis of the emergence and significance of RNA viruses in aquatic animals over the last two decades, with a particular focus on biosecurity and vaccine development.

Keywords: RNA viruses; aquaculture; biosecurity; marine mammals; vaccines; viral emergence.

Figure 2

Biosecurity steps needed to develop site-specific plans for emerging RNA viruses in aquaculture species and marine mammals (captive wildlife). Steps are listed for developing, implementing, auditing, and certifying an effective biosecurity program intended to prevent, control, and possibly eradicate disease in any epidemiological unit: a defined population of animals, separated to some degree from other populations, in which infectious and contagious diseases can be transmitted [22]. Adapted from Scarfe and Palić [18]. Created with BioRender.com.

Figure 3

Spread of highly pathogenic avian influenza virus (HPAI) strains (H5N1 and H5N8) in marine mammals. (A) Marine mammals, including pinnipeds and cetacean species, affected by HPAI H5 virus cases. (B,C) Geographic distribution of HPAI H5 virus cases in marine mammals. Large-scale outbreaks in pinnipeds, particularly sea lions and harbor seals, have resulted in mass die-offs in Chile and Uruguay, with recent reports of infections in cetacean species, such as dolphins. Data from the WAHIS database, WOAH (2020–2025), UK Government [133], and reports from Murawski et al. [136] and Sevilla et al. [137]. Created with BioRender.com.

Figure 1

Emerging viral outbreaks in aquatic species. World Animal Health Information System (WAHIS)-reported outbreaks of emerging and threatening viruses in fish (A) and crustaceans (C) over the last decade (2015–2024). RNA virus outbreaks in fish (B) and crustaceans (D) from 2005 to 2024 (over 20 years). The data indicate that RNA viruses are responsible for the majority (60%) of outbreaks in fish, particularly in cold-water salmonids, whereas they account for less than 1% of outbreaks in crustaceans. Infectious hematopoietic necrosis virus (IHNV) shows a continuous increase in outbreaks, with a slight rise in salmonid alphavirus (SAV) and tilapia lake virus (TiLV) cases. Among wild fish species, viral hemorrhagic septicemia virus (VHSV) and red sea bream iridovirus (RSIV) (15 outbreaks each) are responsible for most reported outbreak cases, followed by koi herpesvirus (KHV) (7 outbreaks) and IHNV (6 outbreaks) over the last decade. DNA viruses, such as KHV and RSIV, pose a major threat to warm-water and mariculture fish species (40% of outbreaks), while DNA viruses white spot syndrome virus (WSSV) and infectious hypodermal and hematopoietic necrosis virus (IHHNV) account for 99% of outbreaks in crustaceans. Temporal trends of RNA virus outbreaks in crustaceans from 2005 to 2024 demonstrate a gradual decrease, with no recorded outbreaks for most viruses since 2024. Data show a significant decrease and even the absence of reported outbreak records in most aquatic species (e.g., infectious myonecrosis virus (IMNV)) during the COVID-19 pandemic from 2020 to 2022. Yellow head disease (YHD) data are available until 2018, and after 2019, only yellow head virus genotype 1 (YHV-1) is recorded. Data are derived from the WAHIS database of the World Organization for Animal Health (WOAH) [7].

Figure 4

Self-assembling protein nanocages as a novel vaccine platform for RNA viruses in aquatic animals. (A) Schematic representation of encapsulin (ENC) nanocages and a detailed view of the monomer with domain organization. (B) Antigen display on encapsulin platforms via genetic fusion of the antigen-encoding gene to the C-terminal region. Encapsulin shell proteins self-assemble into 18–42 nm protein cages composed of 60, 180, or 240 identical subunits. Created with BioRender.com.