Category: Y453F
Preprint: Cluster 5 mink variant demonstrated a reduced sensitivity to neutralizing antibodies in convalescent plasma samples
In Denmark, SARS-CoV-2 variants co-circulating in mink and humans collectively acquired at least 35 different amino acid changes in the spike protein. These SARS-CoV-2 variants belong to lineage B.1.1.298. The receptor binding domain (RBD) substitution Y453F, also observed among Dutch farmed mink, appeared in the first transmission Cluster in June. A two-amino acid residue deletion (ΔH69/V70) in the N-terminal domain appeared together with the Y453F in August 2020 and occurred in the subsequent Clusters 2, 3, and 4. A new variant, termed Cluster 5, with two additional amino acid substitutions, i.e., I692V downstream of the transmembrane protease serine 2 (TMPRSS2)/furin cleavage site and M1229I within the transmembrane domain, was identified in September 2020 on 5 mink farms and in 12 human cases (age: 7–79 years; symptoms: asymptomatic to mild).
Given the potential of this variant to spread among humans, as observed for other mink-associated variants, and an increased risk of antigenic alterations with the multiple spike changes, it was deemed necessary to do a rapid evaluation of this “Cluster 5” variant in vitro. To aid timely public health responses, Statens Serum Institut released a preliminary report on 10 November 2020. A more detailed evaluation of this Cluster 5 variant and its in vitro fitness and neutralization potential is presented here.
Preprint: In vitro Characterization of Fitness and Convalescent Antibody Neutralization of SARS-CoV-2 Cluster 5 Variant Emerging in Mink at Danish Farms
Image vy Otwarte Klatki, CC BY 2.0, via Wikimedia Commons
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Spain: Four new #coronavirus outbreaks at mink farms in Galician province of A Coruña.
The World Wildlife Fund has renewed its calls for American mink farms in Spain to be closed down following the news that another four outbreaks of Covid-19 have been identified at establishments in the Galicia province of A Coruña.
These latest outbreaks bring the total at mink farms in Spain up to 9, including 7 in A Coruña, and the WWF welcome the news that the issue is on the agenda for the current meeting of the European Agriculture and Fisheries Council (AGRIFISH). The organization continues to petition for the forced closure of the 25 mink farms in Galicia, due not only to the proven link between the species and the spread of coronavirus but also to the threat the invasive species represents to native wildlife.
According to the WWF, the Spanish authorities have been slow to take action regarding mink farms, not tightening the controls and checks at these establishments until late last year in contrast with the rapid reactions of other European governments, such as those of the Netherlands and Denmark.
Poland: #coronavirus strain found on a Polish mink farm can be directly transmitted from mink to humans and vice versa
A SARS-CoV-2 strain found on a Polish mink farm can be directly transmitted from the animals to humans and vice versa, the Agriculture Ministry has said. The mink virus variant, the first detected in farm animals in Poland is, up to now, not identical to any of the new strains found recently in humans, but belongs to an animal strain well-known to epidemiologists, the ministry said in a statement on Saturday. It also differs from the strain detected in Danish minks, the ministry added.
The infection on the Polish mink farm in the northern county of Kartuzy was detected in late January. All 5,800 minks have been culled.
Mink: 100% infection, recovery and then 75% re-infection of farmed mink
Poland: new push to ban mink farming in the EU to prevent #coronavirus mutations
The Polish agriculture ministry stated that minks pose a threat of “an uncontrolled spread of the SARS-CoV-2 virus and the formation of dangerous mutations because they are significantly susceptible to infection by this virus”.
Poland has joined forces with other EU countries to push the European Commission into banning mink farming in Europe because of the COVID-19 threat the animals pose to humans and wildlife, the Agriculture Ministry stated.
Mink: 100% infection, recovery and then 75% re-infection of farmed mink
Ireland: fur-farming including mink to be banned in 2022 to prevent #coronavirus zoonosis
The Irish Cabinet is set to agree to ban fur-farming from next year, with a compensation package for farmers also expected. There are approximately 120,000 mink on three farms in counties Laois, Donegal and Kerry. The Cabinet will be told that the three farmers will be compensated for the closing down of their operations with asset value, earnings, redundancy payments and demolition fees to be considered in the package.
Minister for Agriculture Charlie McConalogue will today (Tuesday) bring a memo to Cabinet on the prohibition of fur-farming in Ireland, which will begin early in 2022 to allow the farmers see out the 2021 season.
Sweden: farmed mink outbreaks saw mink infecting humans with #coronavirus
A majority of genome sequences from human cases had clear phylogenetic relationships to sequences recovered from mink samples. Sequences from humans and mink from the same mink farms clustered closely together, suggesting within-farm human-to-mink and/or mink-to-human transmission. In sequences from two human samples from one of the negative mink farms the mutation Y453F, considered as an adaptation to mink, was observed.
“Between mid-October and mid-November, the National Veterinary Institute received 74 submissions of between 3–5 dead mink, representing between 1 and 4 submissions per farm. Thirteen farms gave positive results for SARS-CoV-2 nucleic acids using qRT-PCR. All positive farms were located in Sölvesborg, the County of Blekinge, in the south-eastern part of the country. None of the positive farms had reported increased morbidity or mortality before testing positive but, retrospectively, a slight increase in daily mortalities could be observed in the records from several of the farms.
All sequences from mink belonged to sub-lineage B1.1.39, a sub-lineage only seen once in Sweden before the outbreak. From the serological screening, 24 samples per farm were received from 26 out of the 28 mink farms that remained after the pelting. Specific SARS-CoV-2 antibodies were detected in the vast majority of samples from 23 farms, including in all farms that previously had been tested positive for SARS-CoV-2 nucleic acids. In the remaining three farms, all samples tested negative.
A total of 100 persons have been registered in the program, but due to the seasonal mode of work, and changes in the workforce, the number of participants has varied. The 317 samples that have been taken and analysed for ongoing viral infection within the surveillance program have resulted in 8 positive persons. In addition to samples from these persons another 14 samples from mink farmworkers that was tested positive before the surveillance was launched were collected. All 22 samples were whole-genome sequenced (WGS). In the serological survey, 78 persons participated, among whom 27 tested positive.
The resulting sequences from WGS were analysed using pangolin. Generally, two main groups were seen, one representing sequences with a pangolin classification similar to that of sequences recovered from WGS of samples from minks (B.1.1.39) and the second group representing sequences with a pangolin classification identical to those circulating in Sweden at the time. The sequences were further analysed by aligning them towards the reference sequence NC_045512. A phylogenetic tree was calculated, and the subtree representing sequences with the pangolin classification B.1.1.39 was studied separately as new sequences were added.
A majority of sequences from human cases had clear phylogenetic relationships to sequences recovered from mink samples. Sequences from humans and mink from the same mink farms clustered closely together, suggesting within-farm human-to-mink and/or mink-to-human transmission. In sequences from two human samples from one of the negative mink farms the mutation Y453F, considered as an adaptation to mink, was observed.”
From: Mink-associated infections with SARS-CoV-2 –
Surveillance of infectious diseases in animals and humans in Sweden 2020 (PDF file)
** Update ** Mink farming was suspended for 2021 in Sweden, but on the basis of this report, mink farming should be banned entirely, not just in Sweden, but internationally. Mink farms risk becoming major reservoirs of Sars-CoV-2 capable of spilling back into the human population. The advantages of mink farming do not remotely outweigh the risks.
CDC: possible reverse zoonosis in Michigan mink farm #coronavirus outbreak
Mink: 100% infection, recovery and then 75% re-infection of farmed mink
Denmark: Sars-CoV-2 #coronavirus spike mutations arising in Danish mink – the Cluster 5 report
This study investigates the amino acid changes in the spike surface glycoprotein that appeared during this outbreak [in mink] and their effect on the antigenicity of the SARS-CoV-2 virus.
Spike mutations
Within the infected mink, the SARS-CoV-2 virus mutated, giving rise to several amino acid changes in the spike protein. The first was a tyrosine to phenylalanine at amino acid 453 (Y453F), a mutation that also appeared during the Dutch mink farm outbreaks. It is a conservative amino acid substitution in the receptor binding domain that directly contacts the host ACE2 receptor at amino acid 34 (Wang et al). This ACE2 contact position differs between human and mink (histidine [34H] in humans and tyrosine [34Y] in mink and other mustelids (Damas et al)), which suggests that Y453F is an adaptation mutation to mink ACE2. Importantly, 453F increases affinity for human ACE2, which may explain its successful introduction and establishment in humans.
Following the appearance of 453F, additional spike mutations were observed in minks and the humans epidemiologically linked to the infected mink farms (Fig. 1). These include: i) 69-70deltaHV – a deletion of a histidine and valine at amino acid positions 69 and 70 in the N-terminal domain of the S1 subunit; ii) I692V – a conservative substitution at position 692 that is located seven amino acids downstream of the furin cleavage site; iii) S1147L – a non-conservative substitution at position 1147 in the S2 subunit; and iv) M1229I – a conservative substitution located within the transmembrane domain.
Denmark’s SSI: The Cluster 5 report (PDF download)
Denmark: work begins to exhume millions of #coronavirus contaminated mink
Two dead wild mink infected with #coronavirus found in Castellon, Spain
Mink: 100% infection, recovery and then 75% re-infection of farmed mink
SARS-CoV-2 #coronavirus variants from mink evade inhibition by antibodies
“Our results show that one of two antibodies from an antibody cocktail used for COVID-19 therapy no longer efficiently inhibits the viral variant with the Y453F mutation. Furthermore, our study demonstrates that the Y453F mutation reduces inhibition of the virus by antibodies produced by COVID-19 patients. This means that people who were infected with SARS-CoV-2 may have reduced protection against mink variants of the virus,” says Markus Hoffmann