Study identifies an unknown SARS-CoV-2 lineage on three mink farms in Poland

In a recent study published in the Eurosurveillance Journal, researchers detected a cryptic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage on mink farms in Poland.

Study: Cryptic SARS-CoV-2 lineage identified on two mink farms as a possible result of long-term undetected circulation in an unknown animal reservoir, Poland, November 2022 to January 2023. Image Credit: Aninspiration/Shutterstock.com

Background

During the coronavirus disease 2019 (COVID-19) pandemic, mink production took a major hit worldwide, especially after reports of human-to-animal SARS-CoV-2 transmission and reverse spillover.

However, unlike Denmark and the Netherlands, where they culled minks, Poland did not. Accordingly, Poland emerged as the largest mink producer in Europe.

However, Poland's number of mink farms decreased dramatically, from 350 to 166, between 2019 and 2023. Issues with pelt import and declining demand for fur worldwide drove this decline.

About the study

In Poland, they began testing all mink farms using a novel scheme from December 2021 onwards to detect SARS-CoV-2 in animals when farm animals began to show disease symptoms, started dying, or workers tested COVID-19-positive.

They collected oropharyngeal swabs for real-time reverse transcription-polymerase chain reaction (RT-PCR) assays from three farms (Farms 14, 16, & 17) located in a lowland agricultural area but in an 8 km range.

The researchers identified the first positive farm in January 2021 and 13 more farms by July 2022. Between September 2022 and January 2023,  they identified three more positive mink farms, Farms 14, 16, and 17.

The team collected samples to perform whole genome sequencing (WGS), the sample size of which detected between 50% and 5% prevalence, respectively, with 95% confidence. WGS helped the researchers gather data on changes in SARS-CoV-2 genomes detected in minks.

Further, the researchers tried to locate potential sources of SARS-CoV-2 entry into minks. So, they performed interviews and site visits per the procedure described in the Sikkema et al. study. The team could not do serological investigations; thus, they had no clue whether minks that tested positive (in this study) were ever-infected in the past. 

Results

The researchers identified 14 SARS-CoV-2-positive mink farms, where four types of SARS-CoV-2 variants belonging to eight Phylogenetic Assignment of Named Global Outbreak (PANGO) lineages caused infections. Further, the researchers detected a novel, cryptic SARS-CoV-2 lineage in a short duration of three months on two mink farms in close geographical proximity.

Phylogenetic analyses revealed that viruses from both mink farms formed a cluster closely linked to B.1.1.307 virus genome sequences retrieved from this Polish region and different parts of Europe nearly two years ago from human COVID-19 cases; however, with >40 single nucleotide polymorphisms (SNPs).

The viruses detected on mink farms were nearly identical, but with several mutations not found in the Wuhan-Hu1 strain and human B.1.1.307 SARS-CoV-2, including F486L and N501T in the spike (S), which suggested viral evolution in minks.

Other mutations were amino acid substitutions and deletions at F486L, N501T, W64L, T572I, and S929I positions and positions 140–143, respectively.

Negative RT-PCR test results for farm workers and owners' families ruled out the possibility of a chronic viral shedder who introduced SARS-CoV-2 to mink. An undetermined animal source likely introduced the virus into minks.

On all three farms where minks tested SARS-CoV-2-positive, minks might have come in contact with cats or other wild carnivores, who likely served as intermediate hosts for SARS-CoV-2.

The researchers observed that all three SARS-CoV-2-positive farms had a concrete fence 1.8 m high with no holes for wild animals to enter. However, trees on both sides that reached across provided a potential route for entry into farms.

In addition, there were other barriers to protect farm minks, e.g., wire mesh cages on poles without walls. At the farm entrance, there were corrugated metal gates.

Interviews with staff and farm owners confirmed the sporadic presence of wild carnivores, e.g., foxes, on the mink farms. In addition, they mentioned that wild bird species also occasionally visited these farms. Though the farm's employees were not aware of any escaped minks, some might likely have escaped.

Another possibility is that a free-living mink introduced SARS-CoV-2 into farm minks; however, this hypothesis needs testing. On the other hand, the researchers were sure that encounter with the virus was recent.

The SARS-CoV-2 strain detected in farm minks differed from human-infecting SARS-CoV-2 only by 40 nucleotides, which indicated that it was acquired recently and evolved rapidly.

Minks on the SARS-CoV-2-positive farms did not have typical disease symptoms, which raised the likelihood of independent viral evolution and a potential source for novel strains that could cause new outbreaks.

To date, they could not detect spillback of the identified cryptic SARS-CoV-2 lineage into the human population. There were no bats on the mink farms. However, the team found feral cats on all mink farms examined during the study. Testing of feral droppings for SARS-CoV-2 returned negative results.

Conclusions

Despite a marked reduction in mink farms, they still exist in Poland, serving as breeding grounds for human-to-animal and reverse spillover of SARS-CoV-2. The study highlighted the need for increasing the frequency of routine SARS-CoV-2 surveillance on mink farms, especially since the animals were asymptomatic.

Importantly, Polish authorities should strengthen testing for farm workers, owners, and their families. In addition, there should be sporadic molecular and serological testing of wild animals, such as feral mink, cats, martens, foxes, etc.

In the absence of mandatory surveillance, locating the source of viral entry becomes unfeasible, and they remain undetected. As the study demonstrated, relying alone on passive surveillance after the symptomatic outbreak was inadequate.

Written by

Neha Mathur

Neha is a digital marketing professional based in Gurugram, India. She has a Master’s degree from the University of Rajasthan with a specialization in Biotechnology in 2008. She has experience in pre-clinical research as part of her research project in The Department of Toxicology at the prestigious Central Drug Research Institute (CDRI), Lucknow, India. She also holds a certification in C++ programming.