DNA-based Monitoring of Whirling Disease
DNA-based Monitoring of Whirling Disease

DNA-based Monitoring of Whirling Disease


Picture 1
©STREAM 2020


Freshwater fish species are under increasing pressure from human-related activities in watersheds across Canada. For salmonid fish however, there is a greater threat of the biological kind. Whirling disease is a disease caused by a microscopic parasite, Myxobolus cerebralis, that affects salmonid fish, namely some species of trout and whitefish.

Transmission, Symptoms and Distribution

The whirling disease parasite has a complex life cycle that requires multiple hosts. The first host is a species of aquatic-worm, a sludge worm (Tubifex tubifex), which ingest the spores of Myxobolous (Myxospores) and subsequently become infected. The second and final host are species of salmonid fish, which become infected through either eating infected worms or directly through free-swimming Triactinomyxons (TAMs), produced by the parasite when inside the worm and shed into the surrounding water. These TAMs infect the fish by attaching to the skin or gills and migrate to the cartilage, where they feed, multiply and develop into spores.


Picture 2
Life cycle of parasite Myxobolus cerebralis. Picture credit: Alberta Environment and Parks.

Species such as rainbow trout, cutthroat trout and whitefish are particularly susceptible to whirling disease, and the severity of whirling disease depends largely on the age and size of the salmonid host. Mortality rates for young fish (most vulnerable age) can reach up to 90%. Salmonid fish have a high socioeconomic importance, due to the large commercial and sport fisheries based on these species. This means the effects of whirling disease can be very profound, both ecologically and socioeconomically.


Typical clinical symptoms of whirling disease include: 1) Deformities in the jaws, head, gill cover, body, and/or tail; 2) Characteristic whirling swimming behaviour; 3) Darkening of infected fish tails due to nerve compression.

Map of the four major watersheds in which whirling disease has been confirmed. Picture credit: Alberta Government.



There are currently no known treatments for whirling disease and considering that Myxospores can remain viable in sediment for up to 20 years, this disease is particularly difficult to manage.

In Canada, whirling disease has been declared in 4 major watersheds in central and southern Alberta.

Management and DNA Metabarcoding

With whirling disease being a complex disease, preventing the introduction of the parasite to new water bodies and preventing infection of healthy fish populations is currently the best option for managing the disease. Due to the multi-host nature of Myxobolous, one method of monitoring the spread of the infection is to monitor the distribution of sludge worms (T. tubifex) across the infected watersheds. An easy way to do this is by collecting benthic samples and analysing them using DNA metabarcoding.

DNA metabarcoding is becoming a common method of assessing freshwater biodiversity of macroinvertebrates and forms the foundation of the STREAM project. In terms of STREAM, this approach involves the collection of benthic samples via kick-net methodology following CABIN protocols. Once in the lab, samples have DNA extracted, are sequenced using a next-generation sequencing (NGS) platform and macroinvertebrates are identified by comparing results with a DNA reference library.

Picture 5
Bow River in Alberta, Canada is a ‘Red Zone’ for whirling disease. Picture credit: Alberta Environment and Parks.

In 2019, the STREAM project undertook a sampling program to collect data on benthic macroinvertebrates in the Bow River Basin. The Ghost Watershed Alliance Society (GWAS), a Watershed Stewardship Group (WSG) based in Alberta, partnered with the STREAM and sampled a creek within the Ghost Watershed, a sub-basin of the Bow River. GWAS’ vision, in part, is for the Ghost Watershed to be a biologically rich headwaters ecosystem in Alberta’s Eastern Slopes. Through the STREAM project, GWAS wanted to begin building a baseline of the macroinvertebrate communities, including indicator groups such as mayflies (Ephemeroptera), stoneflies (Plecoptera) and caddisflies (Trichoptera; commonly referred to as EPT groups), which are present in a section of the Bow River Basin.

Bow River DNA Results

In combination with an additional sample collected by University of Calgary, a total of four sites were analysed within the Bow River area, two of which were within the ‘Red zone’ for whirling disease.

Results indicated that traditional bioindicator EPT species, such as spiny crawler mayfly (Ephemerella tibialis) and small minnow mayfly (Baetis tricaudatus) were detected in three out of the four sites (excluding BOW01). In addition, DNA from the Myxobolous parasite worm host (T. tubex), was detected exclusively at site BOW01A.


Picture 7
Members of GWAS at CABIN Training and Certification event with WWF-Canada Freshwater Specialist, Catherine Paquette (left) and Living Lakes Canada STREAM program manager, Raegan Mallinson (second from right). Picture credit: GWAS.

The application of DNA metabarcoding for detecting the presence of a parasite host is particularly important, especially for a complex disease such as whirling disease. There have been known cases of infected salmonids at BOW01A but not at BOW01, which, when combined with the DNA data for sludge worm presence, suggests that whirling disease could potentially be more localised than previously thought.

In 2020, GWAS hopes to expand their circle of volunteers and get more people involved in the sampling process, to generate more data for better understanding the health of the watersheds in their area. Bob from GWAS has stated how STREAM has “stretched our thinking to be more strategic about how we prioritize sampling locations and schedule this work as part of a more comprehensive multi-year research approach for our watershed.” The STREAM approach using DNA metabarcoding in conjunction with community groups stretches beyond simple ID of macroinvertebrates now. Through partnering with groups such as GWAS, we can begin to ask and answer bigger ecological questions and better understand ecological processes such as disease transmission, which is vital for better understanding freshwater health.


To find out more about the important work conducted by the Ghost Watershed Alliance Society, visit their website here and read their guest blog about their experiences with training and sampling on the STREAM website here.

For more information on whirling disease, visit the Alberta Environment and Parks website here.


By Dr. Chloe Robinson (Postdoc and STREAM project manager)


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