Denmark: Omicron, BA.1 and BA.2 Risk Assessment for January 2022

The full document “Risk assessment for the development of the Covid-19 epidemic” from Denmark’s SSI, dated 22nd January 2022, translated into English. Includes details of Omicron, BA.1, BA.2 infections.

 

Risk assessment for the development of the Covid-19 epidemic translated

 

The chart below is from the report:

Figure 2 shows the development in the Covid-19 related hospital occupancy per day divided into total, psychiatry, intensive care and hospitalized on a respirator. Figure 2 shows that an increasing proportion of the inpatients are patients admitted to a psychiatric ward.

SSI Risk Assessment web page (in Danish)

SSI Risk Assessment PDF download (in Danish)

 

 

 

 

Image by iris Vallejo from Pixabay

Denmark: 715 Covid deaths in the double and triple vaccinated, 607,000 breakthrough infections

From a vaccinated population of around 4.7 million people, 715 double and triple vaccinated individuals have died of Covid-19 in Denmark. There were a further 326 deaths in people with a single dose of vaccine, making a total of 1,041 breakthrough deaths.

434,803 people who have received two doses of vaccine have had breakthrough Covid infections, and 105,271 people with booster doses have also had a breakthrough infection. A further 67,749 infections in people with a single dose of vaccine, making a total of 607,823 breakthrough infections.

Breakthrough infections seem to be running at about 150,000 a week in Denmark.

 

 

 

Denmark’s SSI Breakthrough infections and vaccine efficacy report (In English and Danish)

SSI Webpage (in English)

 

Denmark: About 75% of Covid hospitalizations are fully vaccinated *13 UPDATES*

Cattle infected with Covid

Eleven cows from different farms in Germany test positive for Sars-CoV-2.

Here, we serologically investigated 1000 cattle samples collected in late 2021 in Germany. Eleven sera tested antibody-positive, indicating that cattle may be occasionally infected by contact to SARS-CoV-2-positive keepers, but there is no indication of further spreading.

All bovine samples were tested by an RBD-based multispecies ELISA performed as described previously. During the initial test validation and during an experimental SARS-CoV-2 infection study in cattle, it could be shown that the ELISA does not cross-react with the bovine coronavirus (BCoV)

Resulting double infections of individual animals could potentially lead to recombination between both viruses, a phenomenon well-described for other coronaviruses. Although, the emergence is highly unlikely due to the low susceptibility of cattle for SARS-CoV-2, a conceivable chimera between SARS-CoV-2 and BCoV could represent an additionally threat. Hence, also ruminants should be included in outbreak investigations and regular screenings should be performed to exclude any spread of new variants in the livestock population.

Biorxiv Preprint: Serological screening suggests single SARS-CoV-2 spillover events to cattle

 

UPDATE 1 – 26th January 2022:

From a separate study:

“In this study, none of the animals shed detectable infectious virus during the course of the study, while several individual animals (1 calf, 2 goats, and one rabbit) had RT–PCR positive nasal and/or oral swabs, which suggests that these animals may be minimally permissive to infection. Live virus was isolated from the trachea of one calf necropsied on 3 DPI, but no other tissues were positive in that animal, suggesting local infection of the upper respiratory tract during acute infection.”

Susceptibility of livestock to SARS-CoV-2 infection (Angela M. Bosco-Lauth et al)

 

UPDATE 2 – 26th January 2022

“Investigations on ACE2 polymorphism indicate that the list of SARS-CoV-2 susceptible species may also include the Macaca mulatta (monkey), Felis catus (cat), Canis lupus (dog), Oryctolagus cuniculus (rabbit), Mustela putorius furo (ferret), Mesocricetus auratus (hamster), Bos taurus (cow), Bubalus bubalus (buffalo), Capra hircus (goat), Ovis aries (sheep), and the Mustelidae family (minks), all found to be susceptible to SARS-CoV-2 infection and the virus was efficiently transmitted from one infected animal to another via respiratory droplets.”

Coronavirus Evolution, Cross-Species Transmission and Recombination

 

 

Sars-CoV-2 – checkmate to the virus in four moves

 

 

 

Photo by Doruk Yemenici on Unsplash

Israel: 4th vaccine dose recommended for all adults

A panel of health experts advising the Israeli cabinet on the fight against the coronavirus pandemic has recommended that a 4th vaccine dose be administered to the population over the age of 18 if at least five months passed since receiving the third jab.

Ynetnews.com report

 

 

Israel: Fourth dose of vaccine gives limited protection against Omicron infection

 

 

 

Photo by Towfiqu barbhuiya on Unsplash

Hong Kong: Thousands of hamsters, rabbits, chinchillas and guinea pigs killed to prevent Covid outbreak

More than 2,000 hamsters, guinea pigs, rabbits and chinchillas have been euthanised after some that were imported from the Netherlands were found to be COVID-positive.

A range of small animals found in pet shops with the imported hamsters were seized and put down by authorities, including guinea pigs and rabbits.

Hong Kong authorities said Sunday that just one of over seventy hamsters handed in by pet owners for a COVID cull has tested positive, as thousands of city residents remain under lockdown to combat an outbreak.

The AseanPost.com report

 

 

 

Photo by Arif L on Unsplash

Omicron can survive longer on human skin and plastic

The Omicron COVID-19 variant can survive longer than earlier strains of the virus on plastic surfaces and human skin, new research by Japanese scientists has found.  The study by a team from the Kyoto Prefectural University of Medicine, which is not yet peer reviewed, found that the variants survived much longer than the original strain following a series of laboratory tests.

Euronews report

Biorxiv preprint: Differences in environmental stability among SARS-CoV-2 variants of concern: Omicron has higher stability

 

 

 

Image by Zhivko Dimitrov from Pixabay

WHO: The end of the pandemic is plausible

The Covid-19 pandemic has entered a new phase with the Omicron variant, which could infect 60 percent of people in Europe by March, and could bring it to an end, the WHO Europe director said Sunday. “It’s plausible that the region is moving towards a kind of pandemic endgame.”

 

Really? Has anyone told the virus yet?
This is Europe:

This is America:

This is South America:

This is Asia:

 

This is the WHO:

 

The WHO have played a pretty steady hand during the pandemic so far, but this statement is dumber than a bag of rocks.

 

 

Los Angeles: Just 3 weeks between Covid infection and death

Of 102 deaths in Los Angeles County reported Thursday, 90% involved people who became ill with Covid-19 after Christmas, and 80% were among those who fell ill after New Year’s Day, indicating a high likelihood of Omicron infection, Los Angeles County Public Health Director Barbara Ferrer said.

The death toll was the highest single-day tally since March 10, 2021. It appears that people who are dying from the Omicron variant are deteriorating much quicker than those infected by earlier variants, Ferrer told reporters.

LAtimes.com report

 

 

 

 

Image by David Mark from Pixabay

Serbia: 97.5% Covid positivity rate at a childrens clinic in Vranje

Thirty nine out of 40 children tested for coronavirus at the Children’s Covid Clinic in Vranje were positive for Covid-19 in the past 24 hours, confirmed the Health Center (ZC) in Vranje. The percentage of infection is 97.5 percent. Only one child had a negative test result.

Fourteen children are of preschool age, and 25 are of school age.

Vranjenews.rs report (in Serbian)

 

 

 

Image by Annie Spratt 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?

India: Omicron BA.2 is now at 57% of genome samples, but is Delta rising again?

India has seen quite considerable growth in the BA.2 sub-lineage of Omicron recently, lifting it to about 57% of all genome samples, with BA.1 now declining steadily.

What is surprising, however, is what looks like a recent increase in Delta variant cases, which now account for about 14% of samples according to CoVSpectrum. Delta was found in almost no genome samples at the turn of the year. This apparent increase could be an anomaly caused by the low number of samples submitted in 2022, but it’s something we’ll keep an eye on.

 

A plot using Cornelius Roemer’s lineage comparison app suggests Omicron BA.2 may be heading higher in India by outcompeting BA.1 completely:

 

It’s not clear which sub-lineage, if any, is responsible for a recent rise in Delta cases in India yet.

 

India has seen a large Omicron wave in January 2022, but it hasn’t yet reached the heights of its notoriously difficult Delta wave of Spring 2021.

 

Sri Lanka has also seen a few Delta cases since the New Year:

 

According to the latest SARS-CoV-2 variant report issued by the Sri Lanka Allergy Immunology and Cell Biology Unit of the Department of Immunology and Molecular Medicine of the University of Sri Jayewardenepura, 75 new cases of Omicron and 3 new cases of Delta were detected from 78 samples.

“These 78 samples were sequenced from the 1st 2nd and 3rd weeks of January from the community.” said Dr. Chandima Jeewandara, Director of the Allergy, Immunology and Cell Biology Unit of the Faculty of Medicine. The 78 Omicron cases include a mix of the two main Omicron lineages BA.1 and BA.2.

Different Delta sublineages were detected in the following locations.1 case of AY.98 (Sri Lanka delta sub-lineage) was detected in Thalangama. 1 case of AY.104 (Sri Lanka delta sub-lineage) was detected in Kaduwela. 1 case of B.1.617.2 was detected in Wellampitiya.

Currently, 8% of the sequences of Sri Lanka are BA.2, which was named as a variant of interest by the UK Health security agency.

Newswire.lk report

 

 

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

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Photo by Ravi N Jha on Unsplash

 

UK: Omicron BA.2 declared a Variant under Investigation

The UK Health Security Agency has designated the Omicron variant sub-lineage known as BA.2 as a VUI, or Variant under Investigation*.

Just 53 sequences had been identified in the UK by 10 January, according to the UKHSA, but the variant is already at ~50% of cases in Denmark and has grown rapidly in January.

Sky News report

 

BA.2 is still at fairly low levels in the UK at present:

 

Although confirmed BA.2 numbers in the UK are currently very small, with just 72 cases identified by genome sequencing up to the 8th January 2022, that figure is a tenfold increase from the previous week when it was just 7 cases.

 

The latest estimate for BA.2, again up to 8th January 2022, is 1641.

 

In Denmark, BA.2 represents about 50% of new cases recently:

 

Infections are still increasing dramatically in Denmark, although Omicron waves are levelling off in many other countries.

 

 

Denmark have said that BA.2 in not causing an increase in hospitalizations, but Danish hospitalization numbers have been increasing recently:

 

UPDATE 1 – 21st January 2022: “The UKHSA announced that they had classed BA.2 as being a variant under investigation in a tweet, but this was later hastily deleted.” (Daily Mail)

 

 

Denmark: Omicron sub-variant BA.2 outcompetes BA.1

 

 

 

New Zealand: Isolation period for Covid cases extended to 14 days

New Zealand has extended its isolation period for Covid cases from ten days to 14 days. The extension is in response to the increased infectiousness of the Omicron variant.  Close contacts of cases, who were previously required to isolate for seven days, must now isolate for 10 days.

The change comes after a person in Palmerston North tested positive for the Omicron variant after they were released from a managed isolation and quarantine (MIQ) facility in Christchurch on January 16.  During their isolation period, the person returned five negative Covid-19 tests, but became symptomatic and tested positive three days after they were released.

Stuff.co.nz report

 

UPDATE 1 – 22nd January 2022:

The latest New Zealand Covid measures could see household contacts of a positive case isolating for 24 days.

1News.co.nz report

 

** FULLY PAID ISOLATION OF INFECTED PEOPLE after a confirmed test is the sort of mitigation governments should have been focusing on from the very first day of the pandemic, rather than pinning all of their hopes on the single line of defence of repeated vaccinations. **

 

Some people still infectious with Covid after 68 days

 

 

Image by Mario Hagen from Pixabay

Preprint: SARS-CoV-2 cell-to-cell spread occurs rapidly and is insensitive to antibody neutralization

“Cell-to-cell spread of SARS-CoV-2 showed no sensitivity to monoclonal antibody or convalescent plasma neutralization. These observations suggest that, once cells are infected, SARS-CoV-2 may be more difficult to neutralize in cell types and anatomical compartments permissive for cell-to-cell spread.”

Alex Sigall Lab’s new preprint: SARS-CoV-2 cell-to-cell spread occurs rapidly and is insensitive to antibody neutralization