Europe has seen major changes in coronavirus case rates over the last two months. In many areas of Europe covid case rates have dropped sufficiently to allow restrictions to be eased, but there are notable exceptions. The Covid-19 rate in Spain now appears to be as bad, if not worse, than two months ago, and the Netherlands has seen a dramatic increase in numbers recently.
In the case of both Spain and the Netherlands, the rates increased following the decision to unlock their countries too quickly, and in both cases those decisions have had to reversed within weeks. Greece too appears to be seeing a new wave, and these areas now represent the largest threat to Europe’s strategy to keeping infection rates down.
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.
Here, we report a case of persistent SARS-CoV-2 infection in an immunocompromised patient with chronic lymphocytic leukemia (CLL), asymptomatically carrying infectious SARS-CoV-2 at day 197 post diagnosis. Viral sequencing showed accumulation of mutations over time and indicated major changes in the spike protein, temporally associated with convalescent plasma treatment… Virus eradication is thus far unsuccessful, as weekly performed RT-PCR tests remain positive for SARS-CoV-2, with the last sample acquired on day 333 just prior to submission of this 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.
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.
The Danish Environmental Protection Agency is investigating the area around the Covid-19 infected mink burial pits at Karup and Holstebro. The Danish Environmental Protection Agency have started environmental studies in the area around the graves. So far, geophysical surveys have been made at both Karup and Holstebro, and wells have been drilled, from which soil and groundwater samples are taken.
In addition, the Danish Environmental Protection Agency has taken samples in nearby watercourses, and work is underway to set up permanent measuring stations. Samples will also be taken in Bovtrup Lake before Christmas. The purpose of the current studies is to map the environmental condition in the area before there is any environmental impact from the buried mink.
By comparing the conditions after a possible impact, with the natural conditions in the area, one can map the impact from the buried mink.
“It has been important for us to move out quickly and do the surveys, so we know both the environmental condition in the area before and after a possible impact from the mink,” said the Acting Office Manager at the Danish Environmental Protection Agency
When the results of the studies are clear, they must form the basis for a possible decision on how the risk of pollution can be averted.
The water samples from the boreholes at Karup and Holstebro are used, among other things, to assess the groundwater’s chemical composition, flow direction and flow rate. So far, 4 boreholes have been drilled in Karup and 12 in Holstebro. The difference in number is due to the fact that the geology in Holstebro is more complicated than in Karup. Therefore, more wells are being drilled in this area.
In addition to drilling, so-called geophysical surveys are also made, which provide a detailed knowledge of the area’s geology.
The surface water in the area is examined for nutrients, organic substances and environmentally hazardous substances.
The Danish Environmental Protection Agency expects the first results to be ready at the beginning of the new year.
On a mink farm with about 15,000 animals, over 75% tested positive for SARS-CoV-2 RNA in throat swabs and 100% of tested animals were seropositive. During follow-up studies, after a period of more than 2 months without virus detection, over 75% of tested animals scored positive again for SARS-CoV-2 RNA.
Whole genome sequencing showed that the virus circulating during this re-infection was most closely related to the virus identified in the first outbreak on this farm but additional sequence changes had occurred. Animals had much higher levels of anti-SARS-CoV-2 antibodies after re-infection than at free-testing. Thus, following recovery from an initial infection, seropositive mink rapidly became susceptible to re-infection by SARS-CoV-2.
Anders Fomsgaard, virus researcher and chief physician at SSI, Statens Serum Institut, tells TV2 that there are now 11 cases of B1617 in Denmark, and that they are all connected to countries where the variant is already known. “So there are not 11 different chains of infection and that reassures us. It would not have been so good,” he says.
Denmark has received the first claim for compensation for a death caused by a special type of blood clot, which the authorities link with the Astrazeneca vaccine. The patient compensation scheme has received a total of 29 compensation applications from citizens who have received the Astrazeneca vaccine. A further eight cases concern the Pfizer vaccine. There are no claims for Moderna.
This is stated by Patienterstatningen, which handles cases of compensation for citizens who are affected by serious side effects from e.g. medicines.
After her first vaccination with Astrazeneca, the 43-year-old nurse Tina Sylvester Rohrmann from Nyborg was hit by blood clots in her lungs. She is sure that there is a connection with the vaccine. The doctors at OUH in Svendborg think the same, she says. The Funen nurse fully supports vaccines. Just not the one from Astrazeneca.
Avisendanmark report (paywall)
“We are dealing with a whole new syndrome, called WHITE. We have identified that there is an increased risk in using the vaccine. It gives us a figure on the increased risk with the serious disease cases. About 1 in 40,000 of those vaccinated with AstraZeneca’s vaccine are affected and many die,” says Søren Brostrøm.
“We know a lot more today than we did a month ago. We know that there is a possible biological explanation why AstraZeneca’s vaccine may cause these cases. This suggests a cross-reaction. We know that there is a temporal connection – we see cases 8-10 days after the vaccination, «says Søren Brostrøm, who gradually feels on safe scientific grounds when he now puts into words the Danish decision to stop using the vaccine.
Stunning developments today in relation to the adenovirus vaccines now being marketed for Covid-19, including AstraZeneca’s Vaxevria, and the Johnson and Johnson Covid-19 vaccine. Are adenovirus vaccines now finished?
- The EU Commission has decided not to renew COVID-19 vaccine contracts with AstraZeneca and Johnson & Johnson – Reuters
- AstraZeneca vaccine: Denmark stops rollout completely – BBC report
- EMA to provide further context on risk of very rare blood clots with low blood platelets – EMA
- U.S. FDA to scrutinize vaccine design behind COVID-19 shots linked to blood clot – Reuters
Our opinion: The writing is on the wall for adenovirus vaccines as far as the Sars-cov-2 pandemic is concerned
The task of digging up Denmark’s 17 million culled mink and burning them has been put out to tender. According to the Danish Waste Association, 13 plants across the country have shown interest in bidding for the project.
“Someone has to do it, and since we have the capacity for it, we can just as well bid”, says the North Jutland waste company’s chairman Kristoffer Hjort Storm”.
One of them is the North Jutland company, which according to the chairman of the board can probably receive 60 tonnes of dead animals a day in the form of two wagon loads. “We have decided that the trucks that are to come to Aalborg with the minks must arrive outside our normal opening hours. Then they come directly in and load the minks into our silo, where they are mixed with other waste,” says Kristoffer Hjort Storm.
While the driver may have to keep his nose shut when unloading the dead animals, according to the chairman of the board, it will not give rise to odor nuisances for the citizens. “The minks are burned at high temperatures, and we have many procedures for cleaning the smoke. There will be no odor nuisance from the smoke. We are completely convinced of that,” says Kristoffer Hjort Storm.
The North Jutland waste company also burned a small amount of dead mink back in November, when the decision to kill all mink had been made.
A trial burning of the minks is expected to take place in mid-May. If everything goes according to plan, the burning of the minks will take place continuously from the end of May until July.
The European Court of Human Rights ruled on Thursday that democratic governments can make vaccinations obligatory, in a landmark judgement rejecting complaints brought by Czech families penalised for refusing compulsory jabs for their children.
“The… measures could be regarded as being ‘necessary in a democratic society'” the court ruled, saying that the Czech health policy was consistent with the “best interests” of children.
Our opinion: ** Is there an easier or quicker way of antagonising parents in the middle of a global viral pandemic than encouraging mandatory vaccinations? We can’t think of one. Expect severe blowback **
A large, new survey of 117,670 people from Denmark’s Statens Serum Institut (SSI) showed that PCR tests found 4,069 positive samples but subsequent antigen tests captured only 2,159 of them. 1,910 people received a negative antigen test result, even though coronavirus could be detected in the throat.
Over a period of just over seven weeks from February 1 to March 23, 117,670 citizens received both a PCR test and an antigen test within 48 hours.
According to the PCR test, 4,069 of them were positive. However, the antigen test captured only 2,159 of them. This meant that 1,910 people received a negative test result, even though coronavirus could be detected in the throat.
“Our study shows that antigen testing is quite imprecise in identifying an infected person. We can see that 47% of all those who are actually infected with corona get a negative test result after an antigen test. So they have been tested false negative “, says acting academic director at SSI Tyra Grove Krause about the study.