France: Sars-CoV-2 detected in domestic rabbits

We tested 144 pet rabbits in France between November 2020 and June 2021 for antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

We found one sample seropositive for both antigens and another positive only for RBD. For positive rabbits, at the time of sampling, no particular symptom consistent with SARS-CoV-2 infection was noted by the veterinarians.

MDPI.com study: First Evidence of Natural SARS-CoV-2 Infection in Domestic Rabbits 

 

 

 

Image by Onkel Ramirez from Pixabay

France: Two wild badgers and three martens test positive for Sars-CoV-2

In Brittany, seropositivity for SARS-CoV-2 was detected in five wild mustelids out of 32 animals tested.

In the French region of Brittany, mainly in the department of the Côtes d’Armor, during the first semester of 2021, seropositivity for SARS-CoV-2 was detected in five wild mustelids out of 32 animals tested. Anti-SARS-CoV-2 IgG against at least four out of five recombinant viral proteins (S1 receptor binding domain, nucleocapsid, S1 subunit, S2 subunit and spike) were detected using automated western blot technique in three martens (Martes martes) and two badgers (Meles meles)

All the mustelids studied lived in anthropized and non-isolated rural areas. From one or more index cases, transmission spread directly between mustelids. This is certain for the badgers from Perret, Côte d’Armor.

Biorxiv preprint: Evidence of antibodies against SARS-CoV-2 in wild mustelids from Brittany (France) 

 

 

Cattle infected with Covid

 

 

Image by PBarlowArt from Pixabay
Image by gruberthecat from Pixabay

 

Europe: Another huge Covid wave is building right across the continent

Almost every country in Europe is now seeing a big increase in Covid cases. In many instances, the waves are already higher than the December 2021 wave.

The chart above shows the situation in Europe at the moment. The pandemic seems to have shifted into an entirely different gear. 

The chart below shows a comparison with previous Covid waves:

 

The current wave in Europe is not entirely made up of Omicron cases either. In some countries, more than 50% of cases are still Delta variant.

 

Last year’s winter wave of 2020/2021 showed signs of having had a double peak, one in November/December 2020, the other in January 2021, with a further lift in cases in March 2021, but all of them were on a much smaller scale than this new winter wave:

 

Under the circumstances, removing all Covid mitigations now, as the UK is proposing to do, would be completely insane.

 

So what can we do? Well, we can do what we should have been doing since February 2020!
  • FREE masks – FFP2 minimum
  • FREE testing
  • FREE ventilation installations, particularly schools and shops
  • Full sick pay for self-isolation of up to 14 days
  • Smaller classrooms located across communities to protect our kids
  • Working from home wherever possible
  • Less contact, reducing unnecessary interactions
  • Less meetings, less flights, less travel, less cruises, less holidays
  • Less festivals, less concerts, less sports events, less garden parties
  • Eat a better diet
  • Support each other
  • Stop hoping big pharma will bail us out – they won’t, they can’t

The virus has outsmarted us, it has outwitted us, and it’s winning hands down. It’s hardly surprising given how dimwitted and clumsy our response has been so far.

It’s a pandemic. Do we really have to wait for our fourth or fifth infection to work this simple shit out?

Czech Republic: B.1.640 family cluster identified in Hradec Kralove, East Bohemia

The first case of infection with the B.1.640 coronavirus variant was detected in the Czech Republic, the University Hospital in Hradec Kralove reported. Four members of his family also fell ill.

The infection with variant B.1.640 was confirmed in a 28-year-old man who was initially suspected of having the variant.

The 28-year-old man came on December 19 to Hradec Kralove from Prague, where he worked. The man has not been abroad recently. After four days, he and then four members of his family fell ill. Samples taken from them are sequenced, local sanitary services said.

A spokesman for these services, Veronika Krejczi, said that all infected people showed the classic symptoms of COVID-19 – cough, fatigue, joint and muscle pain, fever. Loss of smell was also reported in two cases. None of the patients were in serious condition. A man infected with variant B.1.640 is not hospitalized.

Polish News report

 

UPDATE 1 – 17th January 2022

The laboratory of the University Hospital Hradec Králové confirmed the first occurrence of another variant of COVID-19 in the Czech Republic in a sample of a man from the Hradec Králové Region. The mutation, designated B.1.640, was confirmed in the laboratory by whole genome sequencing.

“The sample was taken from a man on December 29, 2021 on suspicion of the omicron variant; samples of two relatives are also ready for sequencing. Hygienists are now examining the type of infection in men,” said the director of the University Hospital Hradec Králové, prof. MUDr. Vladimir Palicka, CSc., Dr. hc Sequencing data were provided to the Institute of Molecular Genetics of the Academy of Sciences.

Variant B.1.640 was first detected in the Republic of the Congo in September 2021, and has since been detected in various countries in less than four hundred cases, most of which are reported from France.

Press release from University Hospital Hradec Králové

 

France: B.1.640 declared a VOI after more than 500 cases found

 

 

 

Image by karban from Pixabay

France: B.1.640 declared a VOI after more than 500 cases found

Sars-CoV-2 variant B.1.640 has been reclassified as a Variant of Interest in France after a new risk assessment showed there have been more than 500 cases on the French mainland, with cases also discovered in the UK and Germany. Other countries in Europe, from Africa, Asia and North America, have also detected this variant, which could suggest an onset of diffusion.

Variant 20A/C – B.1.640 – is classified as a VOI from 05/01/2022, and continues to circulate in Metropolitan France: it represented 0.5% of interpretable sequences for Flash Surveys S48 and 49, and 0.6% for Flash S50.

B.1.640 was detected in 12 of the 13 regions of Metropolitan France since the beginning of October 2021. The regions with the most cases have identified are Hauts-de-France (N=189, in particular the Nord department), Île-de-France (N=185) and Normandy (n=152)

 

 

Variant B.1.640 is now classified VOI since the risk analysis of 05/01/2022, on the basis of the continuation of its circulation in France and preliminary in vitro data, indicating a decrease in the effectiveness of neutralization by vaccine or post-infection antibodies, and therefore a possible escape from the immune response. The circulation of B.1.640 continues at low levels in mainland France: 0.1% for the Flash S51 survey and 0.2% for the Flash survey S52.

A total of 437 sequences of VOI B.1.640 have been deposited in the international GISAID database in 05/01/2022, of which 72% come from France (315). The other countries that have identified this virus are the Republic Congo (N=40), United Kingdom (N=21) and Germany (N=19). However, other countries in Europe, from Africa, Asia and North America, some of which have limited sequencing capabilities, have detected this variant, which could suggest an onset of diffusion.

The identified B.1.640 sequences match mostly to the B.1.640.1 sub-lineage. Among these 437 sequences, 21 carry the E484K mutation, characteristic of sub-line B.1.640.2 (i.e. 4.8%, according to GISAID data). If the E484K mutation has an impact on immune response escape, too few cases have currently been detected to draw conclusions about the characteristics of B.1.640.2 compared to B.1.640.1. In this analysis of risk, no distinction will be made between these two sub-lineages.

VOI B.1.640 has also detected in Reunion, with three cases in total, including one case identified as part of the Flash S43 investigation (25-29/10/2021).

The circulation of the 20A/C variant (B.1.640) continues in France, despite the emergence of Omicron. From preliminary in vitro data produced by the National Reference Center for Respiratory Infection Viruses indicate a decrease in the effectiveness of neutralizing antibodies post-infection or post-vaccination, and therefore a possible escape from the immune response. Variant B.1.640 is therefore now classified as a VOI (variant to follow).

The recently discovered sub-lineage B.1.640.2 (aka IHU) now has 21 cases in France. 

Information for this report has been combined from Variant Risk Analysis dated 12th November 2021 and Variant Risk Analysis dated 5th January 2022 (they’re both in French)

 

UPDATE 1 – 17th January 2022

10th March 2021: International Journal of Infectious Diseases – Genomic surveillance of SARS-CoV-2 in the Republic of Congo

 

Czech Republic: B.1.640 family cluster identified in Hradec Kralove, East Bohemia

 

France: new coronavirus variant B.1.640 detected in Finistère, Brittany

 

 

 

 

Image by sollrox from Pixabay

France: new Sars-CoV-2 variant B.1.640.2 with N501Y and E484K detected

Twelve SARS-CoV-2 positive patients living in southeastern France are infected with a variant with atypical mutations. The index case returned from travel in Cameroon.

Their analysis revealed 46 mutations and 37 deletions resulting in 30 amino acid substitutions and 12 deletions. Fourteen amino acid substitutions, including N501Y and E484K, and 9 deletions are located in the spike protein.

This genotype pattern led to create a new Pangolin lineage named B.1.640.2, which is a phylogenetic sister group to the old B.1.640 lineage renamed B.1.640.1. Both lineages differ by 25 nucleotide substitutions and 33 deletions. The mutation set and phylogenetic position of the genomes obtained here indicate based on our previous definition a new variant we named ‘IHU’.

Medrxiv preprint: Emergence in Southern France of a new SARS-CoV-2 variant of probably Cameroonian origin harbouring both substitutions N501Y and E484K in the spike protein



UPDATE 31/12/2021 – from the French Public Health Department

The B.1.640 variant is classified as a variant under investigation (VUM) by Public Health France (at 12/11/2021) as well as by WHO, ECDC and UKHSA. Since December 8, 2021, the B.1.640 lineage has been divided into two sublines: B.1.640.1 and B.1.640.2.

B.1.640.1 corresponds to the sequences of B.1.640 initially detected, and is majority. B.1.617.2* was detected within a cluster at the end of November 2021 in the Provence-Alpes-Côte region Azure.

B.1.640.2 is characterized by the presence of the E484K mutation (one of the targets of the current strategy screening), which is not present in B.1.640.1. The discrimination between these two sub-lineages is not still included in bioinformatic analysis tools. In this risk analysis, no difference is made between the two sublineages of B.1.640 and all cases are considered 20A / C variants B.1.640.

Public Health Document: Mise à jour de l’analyse de risque sur les variants émergents du SARS-CoV-2 du 01/12/2021  réalisée conjointementpar Santé publique France et le CNR des virus des infections respiratoires   (PDF download in French)

*note: we’re pretty sure they mean B.1.640.2 here, not B.1.617.2



UPDATE – 1st January 2021 – from Github

In a similar vein to the recent split of B.1.1.529(Omicron) into two sister sublineages it appears B.1.640 may also have a similar issue with a major group constating of the vast majority of sequences and a small outgroup which appears related but has a very different set of mutations (EPI_ISL_7181977; EPI_ISL_7156959; EPI_ISL_7156955; EPI_ISL_6315910; EPI_ISL_5926666) and includes sequences from France and England, indicating some degree of spread.

Defining mutations (mutations not shared between both groups shown in bold):
Major lineage:
Spike – P9L, E96Q, Δ136-144, R190S*, I210T, R346S, N394S, Y449N, F490R, N501Y, D614G, P681H, T859N, D936H
Non-spike – NSP2 – P129L, E272G; NSP3 – L1301F, A1537S; NSP4 – S386F, R401H, T492I; NSP6 – V149A; NSP12 – P323L; T32I, Q57H; M – I82T; ORF8 – Q27*STOP; N- D22Y, T205I, E378Q; S2m deletion

Minor lineage:
Spike – P9L, E96Q, Δ136-144, R190S, D215H, R346S, N394S, Y449N, E484K, F490S, N501Y, D614G, P681H, T859N, D1139H
Non-spike – NSP2 – P129L; NSP4 – D459N; NSP6 – Δ106-108, T181I; NSP12 – P323L; NSP13 – V371A; NSP14 – P46S, V437F; ORF3a – T32I, Q57H; M – I82S; ORF8 – Q27*STOP; N – D22Y, T205I

Github reportProposal to split B.1.640 into two sublineages

 









 

France: B.1.640 declared a VOI after more than 500 cases found

 

France: new coronavirus variant B.1.640 detected in Finistère, Brittany

 

Image by Rudy and Peter Skitterians from Pixabay

France: 180,000 new Covid cases in one day

While the wave of the Delta variant is not over, Omicron is on the way to asserting itself in France, as in the world. The French Hospital Federation warns that “the most difficult weeks are yet to come”. The number of new cases is exploding: 179,807 have been recorded in the last 24 hours by Public Health France. On this figure there is perhaps a small part of “postponement” following each holiday. The threshold of 100,000 cases had been crossed on Christmas Day.

“Everything suggests that we could reach more than 250,000 cases per day by the beginning of January”, the Minister of Health, Olivier Véran, said during a press conference announcing new measures.

Le Parisien report

 

UPDATE: Spain breaks another record of infections by covid

The Spanish Ministry of Health has registered 99,671 infections in the last 24 hours. The incidence is 1,360.62 cases per 100,000 inhabitants.

El Periodico (in Spanish)

 

 

 

Image by Walkerssk from Pixabay

France, Italy and Spain all see new pandemic record infection figures

France: Covid-19: more than 90,000 cases in 24 hours in France. This is the highest number of daily cases ever since the start of the epidemic in France.

Thursday, December 23, Public Health France announced that the number of contaminations in twenty-four hours amounted to 91,608 cases in the country, a figure never before reached. Over the past seven days, the average was 61,274 cases. The previous highest number of infections was in early November 2020, at the peak of the second epidemic wave, with 86,852 cases.

Le Monde report (in French)



Italy: Daily record of infections since the beginning of the pandemic. Stable deaths and intensive care. There are 44,595 cases of Covid identified in Italy in the last 24 hours , an absolute record since almost two years ago has exploded the pandemic. Yesterday there were 36,293 cases. The previous record was recorded on November 13, 2020, when 40,902 cases were identified.

The swabs carried out are 901,450, the positivity rate is 4.9%. There are 168 deaths. There are 93 admissions to intensive care in 24 hours, bringing the total number of people admitted to intensive care to 1,023. Net of discharged patients, 13 more patients were hospitalized than yesterday. The number of hospitalized patients with symptoms is also rising, 178 more than yesterday and bringing the total of patients in the Covid wards to 8,722.

Il Giorno report (in Italian)



Spain reaches the record of contagions of covid in a day of the pandemic. The infection by coronavirus reached Tuesday the highest figure in so far pandemic to reach their 49,823 cases in the last day and an increased incidence of 86 points to 695, with occupancy in intensive units progressive increase (15.7%) and against the background of new restrictions to slow down the rapid advance of omicron. 

El Periodico report (in Spanish)



UPDATE, 24th December 2021:



 

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

 

 

Maps courtesy of ECDC

 

 

France: confining the unvaccinated “not necessary in France” says Macron

President Emmanuel Macron believes that the health pass allows the French to be protected from the drastic measures taken in Austria.

“The countries that confine the unvaccinated are those that have not implemented the pass. This measure is therefore not necessary in France ”, considers the President of the Republic, who regrets that undecided people are still reluctant to vaccination. “I think we should all be ambassadors for vaccination. I see it, public speaking has its limits. Help me to convince those who are reluctant, who have locked themselves in a solitary distrust ”, adds the latter.

LeParisien.fr report

 

 

 

Image by Paul Henri Degrande 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

France: new coronavirus variant B.1.640 detected in Finistère, Brittany

A new coronavirus variant has been identified in a school in Finistère in October 2021, and named B.1.640.  Twenty-four people, 18 children and six adults in contact with them, have been affected by this new mutation that is unlike any other. A variant so far removed from those in circulation that it took time to identify it.

On October 15, a Covid-19 cluster was identified at Mona Ozouf public elementary school in Bannalec, Finistère. Eighteen students tested positive. As a precaution, two classes are closed out of the twelve in the school. Then two more. And three more. To prevent the spread of the virus during school holidays, the municipality is asking associations to suspend activities.

Further research, by sequencing at Rennes University Hospital, revealed to scientists an “abnormal strain” and “very particular”.  The specimen presents, in fact, multiple unprecedented mutations. Particularly on its Spike protein, the strategic key that allows the virus to enter human cells. A small part of this protein has, in particular, disappeared compared to the forms of the Spike proteins of other variants of the coronavirus.

Le Telegramme report (in French)

 

B.1.640 has already made it onto the ECDC list of variants being monitored, and is listed as originally being sequenced in the Republic of Congo:

 

B.1.640 is also listed in the UK list of variants being monitored:

 

More from France:

 

France: B.1.640 declared a VOI after more than 500 cases found

 

France: new Sars-CoV-2 variant B.1.640.2 with N501Y and E484K detected

 

 

Image by Christel SAGNIEZ from Pixabay

France: Covid facemasks made mandatory in schools again

Schoolchildren in large parts of France were ordered Monday to again wear face masks in class, less than a month after being allowed to remove them, as the country tries to tamp down a surge in Covid cases.

Primary schools in 40 of France’s 101 departments or administrative areas, which had been mask-free for weeks, are affected by the order, which comes a day before President Emmanuel Macron addresses the nation about the health crisis.

Under the government’s Covid protocol, primary school pupils have to wear masks when the incidence rate rises above 50 new infections per 100,000 inhabitants over five consecutive days.

France24.com report

 

Belgium is also reintroducing mandatory masks for some schoolchildren from today. New rules regarding the health safety of pupils will be introduced both in French- and Dutch-speaking schools as of today (Monday), including the re-introduction of face masks for certain age groups.

Brusseltimes.com report

 

France, Germany and Austria are seeing huge increases in Covid case numbers in November 2021:

 

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

 

Image by Marcos Cola from Pixabay

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