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In a recent report made available on bioRxiv * preprint server, researchers from Poland and Finland reveal a contagion event of mink-adapted Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from farmed mink to humans after extensive adaptation process.
Even before the ongoing coronavirus disease 19 (COVID-19) pandemic, coronaviruses were already known as zoonotic pathogens. SARS-CoV-2 is in fact the third highly pathogenic member of this family to appear in the 21st century (after the SARS-CoV and MERS-CoV viruses).
And while mass COVID-19 vaccination activities are currently underway globally, we still don’t know how this pandemic (and its causative virus) will end. In other words, the much vaunted concepts of herd immunity and viral eradication are increasingly seen as unrealistic when prevalence, genetic diversity and ubiquitous animal reservoirs are taken into account.
Different species of mammals around the world are believed to carry SARS-CoV-2 – including dogs, cats, felines, mink, ferrets and deer. In addition, SARS-CoV-2 infections have recently been confirmed in farmed mink in European countries.
Specifically, the cycle of viral transmission from infected mink to humans has been reported in the Netherlands and Denmark. These results are particularly important for Poland, which is the second largest producer of mink skins in Europe.
This is why researchers from Poland and Finland, led by Dr Lukasz Rabalski of the Interuniversity Faculty of Biotechnology at the University of Gdansk and the University of Medicine of Gdansk in Poland, sought to assess whether there is had SARS-CoV-2 fallout from mink farms to humans.
From prevalence assessment to detailed sequences
This study group (alongside other independent groups) recently found active SARS-CoV-2 infection in farmed mink in northern Poland in mid-November 2020. Although the viral prevalence is low and there were only isolated cases, they sequenced the isolates and ruled out any possibility of contamination.
The most recent data acquired and filed by the laboratory of the National Veterinary Research Institute in Poland showed the presence of variants of SARS-CoV-2 from animals located on the same farm. However, subsequent phylogenetic analysis indicated that the virus belongs to the B.1.1.279 lineage (Pangolin classification), which was hardly a surprise given its prevalence in Europe.
In this study, genome sequencing of SARS-CoV-2 was performed at the University of Gdansk in Poland with the use of RNA containing a sample isolated from a positive swab (i.e. say amplification of two target genes with the reverse transcription-polymerase chain reaction).
The resulting reads were then called base, debarcoded, and cut to remove adapter, barcode, and primer sequences, while specific ARCTIC pipeline software was used to generate the SARS- genome. CoV-2. Finally, a phylogenetic analysis was performed with the use of the procedure highlighted in the open source project known as Nextstrain.org.
Close clustering and mutations
In the present study, a case of infection with a variant of SARS-CoV-2 adapted to mink was reported in an asymptomatic human host. Phylogenetic analysis showed that this specific virus clustered closely with viral isolates from mink.
In addition, the researchers found the presence of four mutations in the spike protein gene (which includes the Y453F mutation previously reported as emerging in mink), but also others in an isolate obtained from a patient. positive for SARS-CoV-2.
Mutations specific to the mink-adapted variant were present in the viral genomic sequence, validating the hypothesis that the likely pathway of contraction was from animals. There was also a new mutation previously observed in no SARS-CoV-2 isolate worldwide; this actually truncates an open reading frame (ORF) 7b at position L22.
Epidemiological considerations
The emerging variant described in this study clearly indicates the adaptation of SARS-CoV-2 to the host animal, with some point mutations fixed early in the cycle of transmission between animals and additional changes accumulating over time. .
Although the exact role of mutations remains to be determined, they may provide better suitability for the new host, ”explain the study authors. “It is still not known whether these characteristics modify the course of disease transmissibility or immunogenicity in humans.”
In any case, this variant should be closely monitored in the general population. These results essentially confirm the need for nationwide animal surveillance, as well as careful and genetic analysis of SARS-CoV-2 positive patients.
*Important Notice
bioRxiv publishes preliminary scientific reports which are not peer reviewed and, therefore, should not be considered conclusive, guide clinical practice / health-related behaviors, or treated as established information.
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