Thursday, April 20, 2023

Eurosurveillance: Cryptic SARS-CoV-2 Lineage Identified on Two Mink Farms In Poland



We've an unusual report - published today in the ECDC's Eurosurveillance journal - that describes the discovery of a cryptic lineage of the SARS-CoV-2 virus on two mink farms in Poland, which may have evolved from an as yet unknown host species.

While exquisitely adapted to humans, SARS-CoV-2 has also found a plethora of other suitable hosts, including mink, deer, cats, and even rodents (see Nature: Comparative Susceptibility of SARS-CoV-2, SARS-CoV, and MERS-CoV Across Mammals).

The worry is that new, and potentially more dangerous variants could arise in a non-human host, and then spill back over into humans. It is not just a hypothetical concern, as it has already happened on at least one occasion.

In late 2020 Danish authorities were alarmed to discover several mutated strains of COVID-19 had arisen in farmed mink and had transmitted to humans (see Denmark Orders Culling Of All Mink Following Discovery Of Mutated Coronavirus). 

That emergency was relatively short-lived, as the Alpha variant emerged in Europe in late 2020 and quickly supplanted these mink-variants. But it did illustrate the problem; carriage of SARS-CoV-2 by other host species can produce new variants, which can jump back into humans.

While controversial, there is even some evidence to suggest that the Omicron variant may have evolved after the SARS-CoV-2 virus jumped to mice or other rodents (see Evidence for a mouse origin of the SARS-CoV-2 Omicron variant), and then spilled back into humans. 

For more on this, see Maryn McKenna's Wired article Where Did Omicron Come From? Maybe Its First Host Was Mice.

We've also seen evidence that older COVID variants - no longer circulating in humans - can be maintained in other host populations (see PNAS: White-Tailed Deer as a Wildlife Reservoir for Nearly Extinct SARS-CoV-2 Variants), and may then follow new, and divergent evolutionary paths. 

How often SARS-CoV-2 infects animals in the wild is largely unknown, but the spillover of the virus into other species is increasingly viewed as a serious threat (see WHO/FAO/OIE Joint Statement On Monitoring SARS-CoV-2 In Wildlife & Preventing Formation of Reservoirs)

All of which brings us to today's report.  Due to its length, I've only posted some excerpts, so follow the link to read it in its entirety.  I'll return with a bit more after the break.

Rapid communication Open Access

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  

Katarzyna Domańska-Blicharz1 , Bas B Oude Munnink2 , Anna Orłowska3 , Marcin Smreczak3 , Justyna Opolska1 , Anna Lisowska1 , Paweł Trębas3 , Wojciech Socha3 , Aleksandra Giza4 , Arkadiusz Bomba4 , Ewelina Iwan4 , Jerzy Rola3 , Marion Koopmans2

The widespread circulation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in humans on the one hand and the considerable number of susceptible wildlife hosts at the human–animal interface on the other hand poses a danger of reverse zoonotic spillover into animal populations. This includes wild animals, which could lead to the establishment of novel wildlife reservoirs [1,2]. Mink are especially susceptible and infections have been reported in North America and in several countries in Europe.

Here, we report the detection of a cryptic SARS-CoV-2 lineage on two mink farms in late 2022 and early 2023 in Poland. The closest match was with lineage B.1.1.307 (GR/20B) viruses last detected in humans in late 2020 and early 2021, but the virus detected in mink had at least 40 nt changes, suggesting that it may originate from an unknown or undetected animal reservoir.


Human-to-animal transmission of SARS-CoV-2 and reverse spillover is well documented worldwide [11-13]. After the culling of mink in Denmark and the Netherlands, Poland became the leading producer of mink in Europe and the second in the world after China, despite the major impact of the COVID-19 pandemic on mink production in Poland (a reduction from 350 farms in 2019 to 166 farms in March 2023). Such a decline in the farmed mink population was mainly caused by problems with the export of pelts and, most importantly, a decline in demand for fur around the world.

We describe the detection of a new, cryptic lineage of SARS-CoV-2 on two mink farms. These infections were detected 3 months apart, and the infected farms were in close proximity. The identified viruses were nearly identical and contained a number of mutations versus the Wuhan strain and human B.1.1.307 SARS-CoV-2, including F486L and N501T in the spike protein, which hint towards mink adaptation.
Furthermore, the identified mink SARS-CoV-2 variant was most closely related to B.1.1.307 viruses detected in humans in different parts of Europe more than 2 years earlier. Since all mink farms in the region and also the farm workers and the owners' families have repeatedly tested negative, it is possible that the virus was introduced from some other, undetermined animal host where it may have been circulating undetected. Some of the mutations (486 and 501 in the spike) in the presented isolates have previously been found during prolonged circulation in mink, but involvement of other intermediate hosts like cats or other wild carnivores cannot be excluded and there was a clear opportunity for contact between wild animals and three inspected farm animals.
One possibility is that the virus was introduced from free-living mink which have been found around many farms in past studies [14,15], but this hypothesis needs to be tested. It cannot be ruled out that infection of mink with such a virus occurred quite recently. The identified 40 nt differences from the nearest human virus is not a large and unexpected number, and it is likely that it was acquired during rapid evolution in mink over a shorter period of time.

The animals on the SARS-CoV-2-positive mink farms did not show signs of disease, which creates a possibility of independent viral evolution and may establish a source for future outbreaks with novel strains. Until now, spillback of this cryptic SARS-CoV-2 lineage has not been detected in the human population. The surveillance system for SARS-CoV-2 infections in the region should be strengthened by testing mink and humans on these farms more frequently, but also wild animals such as feral mink and cats and other carnivores such as martens, polecats or foxes should be tested molecularly and serologically.


Despite a notable reduction in the number of mink farms, this type of production still exists in Poland. The monitoring of SARS-CoV-2 infections, which has been introduced for several years, has made it possible to detect 14 positive farms, and the identified viruses were similar to those circulating in humans at the time. However, on the two most recently positive farms, the detected virus was altered to form a new cryptic Pango lineage. Conducting routine surveillance for SARS-CoV-2 on mink farms seems necessary, since the animals described here were asymptomatic, and the viruses would have gone undetected without mandatory viral surveillance. It seems that relying only on passive surveillance in response to symptomatic outbreaks could result in many cases being overlooked.

         (Continue . . . )

For now, there is no indication that this cryptic SARS-CoV-2 variant poses a direct threat to human health, but we many not be as lucky with the next one. 

Eighteen months ago we looked at a perspective article, published in China's CCDC Weekly by two well-known Chinese scientists - George F. Gao and Liang Wang - on the continual spread of SARS-CoV-2 from humans to other animal hosts, and the impacts that could have going forward (see Perspectives: COVID-19 Expands Its Territories from Humans to Animals).

The authors warned that the potential for seeing new and dangerous variants emerge - particularly in wild and domesticated animals - was very high.

Since then we've seen numerous studies showing that the SARS-CoV-2 virus continues to expand its host range, including:

Now that the SARS-CoV-2 virus is no longer constrained by a narrow host range, that provides the virus with plenty of opportunities to reinvent itself going forward. 

Which means we can declare victory if we like, but it will be the virus that will have the last word on the subject.