In a recent report made available on bioRxiv* preprint server, researchers from Poland and Finland reveal a spillover event of mink-adapted severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from farmed mink to humans after an extensive adaptation process.
Even before the ongoing coronavirus disease 19 (COVID-19) pandemic, coronaviruses were already known as zoonotic pathogens. SARS-CoV-2 is actually the third highly pathogenic member of this family to have appeared in the 21st century (after SARS-CoV and MERS-CoV viruses).
And while mass vaccination activities against COVID-19 are currently underway on a global level, we are still not yet sure how this pandemic (and its causative virus) will end. In other words, highly touted concepts of herd immunity and viral eradication are increasingly seen as unrealistic when prevalence, genetic diversity and pervasive animal reservoirs are taken into account.
Different mammalian species around the world were reported to carry SARS-CoV-2 – most notably dogs, cats, felines, minks, ferrets and deer. Furthermore, SARS-CoV-2 infections have been recently confirmed in farmed mink in European countries.
More specifically, the viral transmission cycle from infected mink to humans has been reported in the Netherlands and Denmark. These findings are especially important for Poland, which is the second-largest producer of mink pelts in Europe.
This is why researchers from Poland and Finland, led by Dr. Lukasz Rabalski from the Intercollegiate Faculty of Biotechnology of the University of Gdansk and Medical University of Gdansk in Poland, aimed to appraise whether there were any spillovers of SARS-CoV-2 from farmed minks to humans.
From prevalence assessment to detailed sequences
This study group (alongside other independent ones) has recently shown an active SARS-CoV-2 infection in farmed minks in Northern Poland in mid-November 2020. Although viral prevalence was low and there were only isolated cases, they have sequenced the isolates and discarded any possibility of contamination.
The most recent data acquired and deposited by the laboratory of the National Veterinary Research Institute in Poland showed the presence of SARS-CoV-2 variants from animals located in the same farm. However, subsequent phylogenetic analysis indicated that the virus belongs to the B.1.1.279 lineage (Pangolin classification), which hardly came as a surprise considering its prevalence in Europe.
In this study, SARS-CoV-2 genome sequencing has been performed at the University of Gdansk in Poland with the use of sample-containing RNA isolated from a positive swab (i.e., the amplification of two target genes with the reverse transcription-polymerase chain reaction).
The obtained reads were then basecalled, debarcoded and trimmed in order to delete adapter, barcode and primer sequences, while specific ARCTIC pipeline software has been used to generate the SARS-CoV-2 genome. Finally, phylogenetic analysis has been performed with the use of the procedure highlighted in the open source project known as Nextstrain.org.
Close clustering and mutations
In the current study, a case of infection with a mink-adapted SARS-CoV-2 variant was reported in an asymptomatic human host. Phylogenetic analysis showed that this specific virus clustered closely with viral isolates from minks.
Moreover, the researchers have found the presence of four mutations in the gene for spike protein (which includes Y453F mutation previously reported as emergent in minks), but also other ones in an isolate obtained from SARS-CoV-2 positive patient.
The mutations specific for the mink-adapted variant were present in the viral genomic sequence, validating the hypothesis that the likely route of contraction was from animals. There was also a novel mutation previously not observed in any SARS-CoV-2 isolate around the world; this one actually truncates an open reading frame (ORF) 7b at the position L22.
The emerging variant described in this study clearly indicates the adaptation of SARS-CoV-2 to the animal host, with certain point mutations fixed early during the transmission cycle between animals and additional changes stockpiling over time.
While the mutations’ exact role is to be determined, they may provide increased fitness in the new host,” say study authors. “It remains unknown whether these features alter the course of disease transmissibility, or immunogenicity in human.”
In any case, this variant should be monitored closely in the general population. These results basically confirm the necessity of country-scale monitoring of animals, as well as meticulous and genetic analysis of SARS-CoV-2-positive patients.
bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.