Europe declares Omicron variant B.1.1.529 a Variant of Concern

The ECDC has declared the recently discovered Omicron variant B.1.1.529 as a Variant of Concern in its latest bulletin.

It’s unprecedented for this procedure to happen so quickly. The Omicron variant hadn’t even been named by the WHO when the ECDC listed it as a VOC, underlining the very grave potential for this new virus to overtake Delta as the main variant of concern in Europe in the middle of the existing winter wave.

European Centre for Disease Prevention and Control – variants of concern

 

B.1.1.529 named “Omicron” and designated a Variant of Concern by the World Health Organisation

 

Nu variant: first European case of B.1.1.529 found in Belgium via Egypt and Turkey

Omicron variant: first European case of B.1.1.529 found in Belgium via Egypt and Turkey

A woman with coronavirus symptoms after a trip to Egypt with a stopover in Turkey is the first confirmed case in Belgium of a patient infected with the new variant B.1.1.529, known as ‘Omicron’, initially located by the scientific community in the Southern African countries. She also becomes the first patient in Europe to be infected with the ‘Omicron’ variant.

The diagnosis has been confirmed by the UZ Leuven University Hospital (Leuven) after examining a young adult who was not vaccinated and who began to develop symptoms eleven days after having made the trip to Egypt, according to the Belgian chain RTBF.

This is the first confirmed case in Europe of this variant that is related to southern African countries, although the patient, who has a high viral load, does not seem to have any recent link with that region, according to the information provided by the case.

The diagnosis coincides with a proposal by the European Commission to close the border common to flights with origin or destination in the southern African region, a measure that the 27 have yet to examine on the afternoon of this Friday.

Before the case of the young woman infected in Belgium was revealed, precisely the Belgian Minister of Health, Frank Vandenbroucke, indicated in a press conference that he fully adheres to the proposal to restrict flights to the region for the sake of “prudence“, despite the fact that “not much is known yet” about the variant.

El Periodico report (in Spanish)

 

 

Image by Iwo Bulski from Pixabay

Europe: all-time Covid infection record broken by growing winter superwave

Europe has broken through its all-time high for Covid cases, and is seeing sharp increases in infections right across the continent. The Covid superwave that started in Eastern Europe just one month ago has now spread to all corners of the continent, and doesn’t look like it’s about to break anytime soon.

Virtually every part of Europe is now seeing increases in infections as the winter superwave rolls in.

 

Virtually every government in Europe has pinned its hopes on Covid vaccines preventing further large waves of the disease, a tactic that we have repeatedly warned wouldn’t work. It has been obvious for months that vaccine waning and vaccine breakthroughs would make vaccines a poor first line of defence.

Europe needs to regroup, rethink, and redraw its lines of defence quickly. Greater defence in depth is needed by using mitigations that are proven to work. 

Our estimation of the winter wave of 2020 shown in the diagram below suggests that a wave peak of around 13 – 15 million biweekly cases might have been reached had it not been for the mitigations imposed in Europe and North America in early November 2020.

The 2020 winter wave was broken in half by strong mitigations. It may already be too late to reintroduce them this to year to prevent the worst of the damage from the wave impact.

 

What was the lesson we all learned from earlier waves? Go in hard, go in strong? 

With the half-hearted mitigations that Europe has put in place for the winter wave, it looks as though we are about to find out just how bad things can really get with Covid.

 

Updatable chart for Europe below – press your refresh button to update:

 

Prediction: European Covid winter wave of 2021 will be the worst wave of the pandemic so far

Prediction: European Covid winter wave of 2021 will be the worst wave of the pandemic so far

This isn’t the most difficult prediction we have ever had to make, but there is no doubt that, despite huge vaccination campaigns across the continent, the winter wave now breaking over Europe will be their worst wave of the pandemic so far.

The difference this year is that, despite raging infections in many European countries, despite vaccine waning, vaccine breakthroughs and reinfections, no government is yet considering measures that are strong enough to contain the tide.

Measures including lockdowns and working from home were imposed in many countries across Europe and North America in early November 2020 to prevent the winter wave worsening. Despite their huge unpopularity, the measures, particularly lockdowns, DID work.

The chart below shows our estimation of what the winter wave would have looked like in 2020 without lockdowns. The global winter wave of 2020 was broken in half by lockdowns in key European countries and in North America which made up the bulk of cases.

Our estimation of the size of the Covid global winter wave in 2020. The winter wave was smashed by lockdowns in Europe and North America:

In 2021, however, many countries in Europe have abandoned the use face masks, social distancing and working from home. Lockdowns have been also been ruled out by many governments, fearful of their unpopularity.

 

The chart below shows what the European Covid winter wave looks like on the 4th November 2021. The wave that is forming is virtually identical to the wave of 2020. The difference in 2021 is that there are no mitigations in reserve to prevent previous wave records being broken.  Without urgent mitigations, this wave could be bigger than the one that engulfed India in the spring of 2021

Europe needs to take its head out of the sand, and do it quickly. There are very few tools left in the toolbox to deal with large waves, and every one of them will be needed this year.

We are still waiting for more data to come in to be able to make a prediction on the size of the global winter wave, but it’s not impossible that Europe alone could carry almost the entire burden of the winter wave this year.

Just to be crystal clear then:

  • Vaccines won’t be enough to stop the wave
  • Antivirals won’t be enough to stop the wave
  • Vaccine passports won’t be enough to stop the wave
  • Face masks won’t be enough to stop the wave
  • Locking up the unvaccinated won’t be enough to stop the wave

 

Europe suddenly ablaze with Covid – it could be the biggest wave yet

 

Decoding Sars-Cov-2: How are global Covid waves formed, and can we predict future waves?

 

Image by Brigitte makes custom works from your photos, thanks a lot from Pixabay

WHO: 500,000 deaths from Covid in Europe this winter

“The current pace of transmission across the 53 countries of the European Region is of grave concern,” said regional WHO head Hans Kluge.

Kluge warned earlier that if Europe followed its current trajectory, there could be 500,000 COVID-related deaths in the region by February.

“We must change our tactics, from reacting to surges of COVID-19, to preventing them from happening in the first place,” he said.

Reuters.com report

 

Covid has surged across large parts of Europe again as a winter wave rolls across the continent:

 

 

Photo by Rianne Gerrits on Unsplash

Turkey: 4th vaccination offered to health workers

Turkey’s Health Ministry has announced that health workers and priority groups are now eligible to receive a fourth dose of the COVID-19 vaccine as part of the country’s efforts to combat the resurgence of the disease.

The individuals in these groups who have previously had two doses of the Chinese-produced CoronaVac followed by one dose of the Pfizer/BioNTech vaccine as a booster shot will be able to get one more dose of the Pfizer/BioNTech vaccine.

On July 1 the Health Ministry started to offer a third dose of COVID-19 vaccines for people aged 50 and above and health workers who previously had two doses as part of its vaccination drive.

TurkishMinute.com report

 

280 cases of Delta variant with N501Y, some with E484K too

 

 

 

 

mage by Кирилл Соболев from Pixabay

280 cases of Delta variant with N501Y, some with E484K too

Delta + Alpha + Beta + Gamma recombinant variant found in Turkey.

 

 

 

 

Image by Elliot Alderson from Pixabay

The waxing and waning of the coronavirus pandemic in Europe shows new danger areas emerging

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.

Data maps courtesy of ECDC

 

Spain: 5th wave of coronavirus storms across the country, curfews set to be reintroduced

 

Netherlands: the reproduction R rate is now 2.17 – the highest since February 2020

USA/UK: 2 separate clades of Delta #coronavirus variant with K417N – AY.1 and AY.2

Through routine scanning of variation in Delta, a small number of sequences were detected which had acquired the spike protein mutation K417N. Information suggests that there are at least 2 separate clades of Delta with K417N. One clade is large and internationally distributed with PANGO lineage designation AY.1.  A second clade found in sequences uploaded to GISAID from the USA, now designated AY.2.

As of 16 June 2021, 161 genomes of Delta-AY.1 have been identified on GISAID. from Canada (1), India (8), Japan (15), Nepal (3), Poland (9), Portugal (22), Russia (1), Switzerland (18), Turkey (1), USA (83).

There are currently 38 cases of Delta-AY.1 in England (36 confirmed sequencing and 2 probable genotyping). Cases have been detected in 6 different regions in England. Delta-AY.2 has not been detected in England.

UK Variants of Concern Technical Briefing 15 (PDF download)

 

According to Bani Jolly of the Institute of Genomics and Integrative Biology, the phylogeny of Delta has two separate clades. While AY.1 is found in a few countries including the UK, India and Nepal, the other clade (AY.2), is largely from the sequences from California (USA).

“The split between the two clades seems to be based on two spike mutations — A222V and T95I. While all sequences in the California cluster share spike A222V, all sequences in the larger international cluster share spike T95I,” Jolly tweeted.

Stating that AY.1 has arisen independently a number of times and could be more prevalent than observed in countries with limited genomic surveillance, she tweeted that given that Delta is a variant of concern, it is important to take note of any sub-lineages that may emerge.

Time of India report

 

 

 

Image by PublicDomainPictures from Pixabay

UK: Delta with K417N – the “mountaineers” variant – PHE #coronavirus Delta-AY.1 update

Of the 36 cases of Delta-AY.1 (mountaineers) variant, 27 cases were known to have a vaccination status within the National Immunisation Management System (NIMS). 

“Through routine scanning of variation in Delta a small number of sequences were detected which had acquired the spike protein mutation K417N. Information suggests that there are at least 2 separate clades of Delta with K417N. One clade is large and internationally distributed with PANGO lineage designation AY.1. A second clade found in sequences uploaded to GISAID from the USA. There is limited epidemiological information available at present.

International Epidemiology
As of 7 June 2021, 63 genomes of Delta with K417N have been identified on GISAID. from Canada (1) Germany (1), Russia (1), Nepal (2), Switzerland (4), India (6), Poland (9), Portugal (12), Japan (13), USA (14).

Epidemiology
There are currently 36 cases of Delta-AY.1 in England (35 confirmed sequencing and 1 probable genotyping) plus an additional 10 sequences which include some cases in other UK nations and some genomes for which case data is being sought. The first 5 cases were sequenced on 26 April 2021 and were contacts of travellers to Nepal and Turkey. All these cases were detected in the West Midlands. Cases have been detected in 6 different regions in England (Table 21, Figure 26). The majority of cases are in younger individuals, with 2 cases of age 60 or over (Figure 27). Out of the 36 cases, there were 11 travel associated cases (6 travellers and 5 cases amongst contacts of travellers). Twelve cases have no history of travel or contact with travellers. Countries of travel included red-list countries (Nepal and Turkey), amber-list countries (Malaysia) and green-list countries (Singapore).

Of the 36 cases, 27 cases were known to have a vaccination status within the National Immunisation Management System (NIMS), when linked on NHS number. Of these, 18 cases occurred in people who were not vaccinated, 2 cases in people who had received their first dose within 21 days of specimen date, 5 cases in people who had received their  first dose more than 21 days after specimen date. There was a total of 2 cases where there were more than 14 days between the second dose of vaccine and a positive specimen. No deaths have been recorded amongst the 36 cases.”

PHE download – SARS-CoV-2 variants of concern and variants under investigation in England  – Technical briefing 15 (PDF)

 

UK: The “mountaineers variant” – B.1.617.2 with K417N mutation

 

UK: “Everest climbers could have spread potentially more infectious and vaccine resistant’ variant

 

 

Image by Simon from Pixabay

EU: ECHR throws fuel on the #coronavirus vaccination fire – backs mandatory jabs for kids

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 **

MedicalExpress.com report

 

Photo by CDC on Unsplash

Rapid rise of #coronavirus SARS-CoV-2 spike mutation T478K found in Mexico and several European countries

We report the distribution of the Spike mutation S:T478K and its recent growth in prevalence in the SARS-CoV-2 population. While there is currently no report of association of this variant with clinical features, S:T478K’s rapid growth may indicate an increased adaption of SARS-CoV-2 variants carrying it, particularly lineage B.1.1.222.

The distribution of this mutation is higher in North America, but we could detect it also in several European countries. The location of S:T478K in the interaction complex with human ACE2 may affect the affinity with human cells and therefore influence viral infectivity.

We detected this growth starting at the beginning of 2021, and S:T478K is, at the time of writing (March 26, 2021) characterizing almost 2.0% of all sequenced SARS-CoV-2

An in silico molecular dynamics study on the protein structure of Spike has predicted that the T478K mutation, substituting a non-charged amino acid (Threonine) with a positive one (Lysine) may significantly alter the electrostatic surface of the protein, and therefore the interaction with ACE2, drugs or antibodies, and that the effect can be increased if combined by other co-occurring Spike mutations.

Another experiment showed that T478K and T478R mutants were enriched when SARS-CoV-2 viral cultures were tested against weak neutralizing antibodies, highlighting, at least in vitro, a possible genetic route the virus can follow to escape immune recognition. Everything considered, we believe that the continued genetical and clinical monitoring of S:T478K and other Spike mutations is of paramount importance to better understand COVID-19 and be able to better counteract its future developments.

Biorxiv preprint

 

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EMA: If you have these symptoms after vaccination with AstraZeneca #coronavirus serum seek medical help immediately

“Wheezing, chest or stomach pain, swelling or coldness in an arm or leg, severe headache or worsening or blurred vision after vaccination, persistent bleeding, small multiple bruises, reddish or purplish spots or blisters of blood under the skin” – if you have these symptoms after vaccination against Covid with AstraZeneca serum seek medical help immediately and report that you have recently been vaccinated.

Il Giorno report

 

Image by Usman Yousaf from Pixabay

#SARSCoV2 may be transported by ambient particles especially at sites close to #Covid19 infection hot-spots

According to RT-PCR and 3D-RT-PCR analysis, dual RdRP and N1 gene positivity were detected in 20 (9.8 %) of the samples. The highest percentage of virus detection on PM [particulate matter] samples was from hospital gardens in Tekirdag, Zonguldak, and Istanbul, especially in PM2.5 mode. Samples collected from two urban sites were also positive. Findings of this study have suggested that SARS CoV2 may be transported by ambient particles especially at sites close to the infection hot-spots.

https://www.medrxiv.org/content/10.1101/2021.01.24.21250391v2

 

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