Researchers at the National Centre for Genomic Analysis (CNAG), based at the Barcelona Science Park, have developed the most comprehensive panel of nearly 500 genetic variants for Anisakis simplex to date. This has enabled the design of a low-cost molecular tool for the rapid identification of specimens from the two main Anisakis species found along European coastlines. The study, published in Scientific Reports, is part of a collaborative project with the University of Santiago de Compostela (USC) and the Institute of Marine Research (IIM-CSIC).

Anisakis is one of the marine parasites of greatest concern to public health, as it can cause anisakiasis and allergic reactions when infected fish is consumed raw, undercooked, or without prior freezing. Until now, the limited genetic information available for Anisakis simplex, the most common species in the Atlantic Ocean, has hampered surveillance programmes. Having access to its complete genome will provide a better understanding of how the parasite adapts to its hosts, its evolutionary history, and the mechanisms of hybridisation between Anisakis species, laying the foundation for the development of more effective tools to monitor and control the parasite.

To address this challenge, the Centro Nacional de Análisis Genómico (CNAG) has assembled the most complete genome to date of Anisakis simplex, one of the most widespread species along the Spanish coastline and throughout the north-east Atlantic. The study, published in Scientific Reports, was carried out in collaboration with the Universidad de Santiago de Compostela (USC) and the Instituto de Investigaciones Marinas (IIM-CSIC) with the aim of improving parasite monitoring in both the fishing industry and the seafood supply chain. This genomic resource is particularly valuable for a parasite with such a sophisticated survival strategy. Anisakis exploits the marine food chain to complete its life cycle, passing through plankton, fish, cephalopods and ultimately large marine mammals such as whales.

“Thanks to CNAG’s cutting-edge genomic technologies, we have generated the most contiguous genome assembly to date, including 98.2% of complete genes. The anisakis genome revealed an exceptionally high level of genetic diversity, far greater than we had expected. We identified 150,000 small structural variants in its DNA (insertions and deletions), as well as almost two million single-base variants, in other words, changes affecting a single letter of the genome,” said Dr Tyler Alioto, Genome Assembly and Annotation Team Leader at CNAG and author of the study.

New molecular tool for identifying anisakis

Using the Anisakis simplex reference genome generated by CNAG, researchers at the USC identified a panel comprising nearly 500 genetic variants to investigate both the historical and current population dynamics of the parasite. Building on the analysis of more than 2,000 specimens collected and characterised by the Instituto de Investigaciones Marinas (IIM-CSIC), including Anisakis simplex, the closely related species Anisakis pegreffii , and their hybrids, the researchers developed a low-cost molecular tool capable of distinguishing between the two species while providing new insights into their reproductive and demographic dynamics.

“The development of genomic tools for fisheries management, such as the one developed in this project for anisakis will make it possible to better understand the population dynamics of parasites that affect both human health and commercially important marine species, thereby strengthening prevention and control strategies. This is particularly relevant in an increasingly interconnected world, where parasite dynamics may even cross species barriers and pose a serious risk to public health,” said Dr Paulino Martínez, researcher at the USC and one of the study’s lead authors.

Key insights for fisheries management

Thanks to the new genetic tool, parasites can be accurately classified as Anisakis simplex, Anisakis pegreffii, or hybrids between the two species. Although all three groups are commonly found along the Spanish and Portuguese coasts, where they share the same ecosystems and hosts, their population dynamics and adaptive mechanisms may differ.

“One of the major impacts of climate change on marine ecosystems is marine heatwaves. These events are highly relevant from an epidemiological perspective because many zoonotic agents, such as anisakis, must adapt their developmental strategies by modulating gene expression in response to changing environmental conditions. This has major implications for fish stocks, both in terms of seafood quality, due to parasite migration within seafood products, and for public health because of the immunogenic and allergenic properties of anisakis proteins in different seafood products. This improved genome assembly and annotation of the anisakis genome will enable us to investigate all these questions with much greater precision,” explained Dr Santiago Pascual, researcher at IIM-CSIC and lead author of the study.

The new identification tool is based on 10 genetic variants that distinguish the different groups with high accuracy, making population surveillance studies more effective. These DNA markers have also uncovered previously inaccessible information, including patterns of hybridisation and introgression (the exchange of genetic material between species through their hybrids), as well as genetic differences between populations.

This new knowledge lays the foundations for a deeper understanding of how anisakis populations are distributed across different geographical regions and how they may respond to climate change. In the shorter term, the study will strengthen
parasite surveillance programmes, helping to reduce the risk of anisakiasis in fisheries and throughout the seafood supply chain, while further enhancing the safety of seafood consumption.

» Article of reference: Martínez, P., Casanova-Chiclana, A., Urdaniz, I. et al. Genome assembly and SNP resources of Anisakis simplex enable cost-effective population assessment and discrimination of species and hybrids. Sci Rep (2026). https://doi.org/10.1038/s41598-026-60679-4

» Link to the news: CNAG website [+]