Coronavirus thread

[Karl Henning]

New York covid cases hit record high as omicron spreads and Rockettes, Broadway cancel shows

The 21,027 reported cases were the highest daily count during the pandemic, according to data analyzed by The Washington Post, although testing was less widely available in the early days.

[Florestan]

Spoke again today with my cousin living in South Africa (Johannesburg). No fear-mongering, panic-inducing articles in media of the type we see in Europe and the USA. No lockdown. They just returned from a vacation in Cape Town area: restaurants full, malls full, no Covid Pass. Her son-in-law and granddaughter had omicron: headaches, muscle aches, moderate fever, fatigue, all gone after 10 days of rest, sleep and home treatment.

Looks like the Third World is the place to be right now. 

[Karl Henning]

Highly vaccinated countries thought they were over the worst. Denmark says the pandemic's toughest month is just beginning.

By Chico Harlan
Today at 9:24 a.m. EST

COPENHAGEN — In a country that tracks the spread of coronavirus variants as closely as any in the world, the signals have never been more concerning. Omicron positives are doubling nearly every two days. The country is setting one daily case record after another. The lab analyzing positive tests recently added an overnight shift just to keep up.

And scientists say the surge is just beginning.

As omicron drives a new phase of the pandemic, many are looking to Denmark — and particularly the government institute devoted to testing, surveillance and modeling — for warnings about what to expect.

The emerging answer — even in this highly vaccinated, wealthy northern European country — is dire. For all the defenses built over the last year, the virus is about to sprint out of control, and scientists here expect a similar pattern in much of the world.

"The next month will be the hardest period of the pandemic," said Tyra Grove Krause, the chief epidemiologist at Denmark's State Serum Institute, a campus of brick buildings along a canal.

Ever since the omicron variant emerged in November, the best hope has been that it might cause less severe sickness than the delta version it is competing with, which in turn might make this wave more manageable and help the transition of covid-19 into an endemic disease. But Denmark's projections show the wave so fully inundating the country that even a lessened strain will deliver an unprecedented blow.

Scientists caution that the knowledge of omicron remains imprecise. Denmark's virus modelers have many scenarios. But even in a middle-of-the-road scenario, Danish hospitals will soon face a daily flow of patients several times beyond what they've previously seen.[emphasis mine—kh]

"This will overwhelm hospitals," Grove Krause said. "I don't have any doubt about it."

In her office building, where she works with a six-person modeling team, she tried to explain why omicron amounts to such a setback in the fight against the pandemic. She likened the virus to a flood, and she described how vaccines, under earlier variants, had acted like two barrier walls safeguarding the health system. One barrier resulted from the vaccines' ability to reduce the probability of infection, keeping spread low. The other barrier stemmed from the diminished likelihood of severe sickness and death. Both barriers had some holes, but together, they ensured that the floodwaters never got too high.

But now, she said, the first barrier has been largely removed. Denmark's data shows people with two doses to be just as vulnerable to omicron infection as the unvaccinated. Those who've received boosters have better protection — a sign of hope — but meanwhile, about 3 in 4 Danes have yet to receive a third dose, making the majority of the country vulnerable.

That dynamic, coupled with a variant far more transmissible than the one from last winter, means any Danish person is now dramatically more likely to come in contact with the virus — including the old and the frail, as Denmark's demographics skew older, like much of the West. The water will now flow through the holes in the second wall.

On her double-monitor computer, Grove Krause pulled up the institute's latest projections, which scientists were still tweaking before releasing them to the public on Saturday. The range of possibilities is wide, but the very best scenario — which is unlikely, she said — shows daily hospitalizations matching the peak of last year. In most of the other scenarios, the numbers soar into the stratosphere.

Denmark's hospitals have never had more than 1,000 covid 19 patients at any given time, last winter's peak. But by early January, in a moderate scenario, hospitals could be seeing 500 new covid patients arriving every day. If omicron's transmissibility winds up on the higher end, and it proves just as severe as the delta variant, with a strong ability to evade vaccines, daily admissions could reach 800.

And then there is the matter of infections. Before this wave, Denmark had never seen more than 5,000 cases in a day. On Friday, it logged more than 11,000 new cases. Within a week, in a moderate scenario, case numbers could hit 27,000. And into January? The institute's estimates climb higher still, off the Y-axis.

With the surge coming into view, Denmark this month cut the opening hours for bars and restaurants, urged people to work from home, and closed schools seven days earlier than planned for Christmas break. Grove Krause cautioned that the projections didn't take into account the government's further moves announced Friday, which include the closure of cinemas and theaters. But even a full lockdown, she said, "won't stop this from getting out of control."

Denmark's projections are taken seriously around the world, because they are informed by an all-encompassing coronavirus surveillance system designed specifically for moments like this — when the nature of the virus is quickly shifting.

The system starts with testing: Denmark swabs more people than almost any other country — at a per capita pace seven times that of the United States. The tests, which are free for both citizens and travelers, then arrive at the State Serum Institute, as well as at a sister facility on the other side of the country. Lab technicians identify the positives within 24 hours. And by the following day, they know which variant is responsible for every case.

A portion of the positives are then fully genetically sequenced, delivering an extra layer of insight — allowing researchers not only to see mutations, but also to potentially understand who infected whom.

"We're seeing things pretty much in real time," said Arieh Cohen, head of development at the lab that processes test results and conducts the initial variant analysis.

What that data has shown, so far, is that the hospitalization rate is slightly lower for omicron than it is for delta — though because hospitalizations lag behind infections, and because omicron infections hit only recently, scientists say the results will be more meaningful in a couple of weeks.

Scientists have also identified how omicron was seeded throughout the country, first from travelers inbound from Africa, and then through several superspreader events. A just-published paper from the institute and other researchers described a Christmas party attended by about 150 people. Most were vaccinated. And yet 71 tested positive for omicron.

Initial omicron cases in Denmark have been concentrated disproportionately among people in their 20s — an age group that normally has mild symptoms, and whose infections might be missed by countries that test less. Some scientists at the institute think Denmark's wave is a week or two ahead of other Western countries. But others say many countries could already be experiencing the same pattern, with the young — who are most likely to travel and socialize — jump-starting community spread.

"There's a chance that Denmark is capturing the spread that other countries are missing," said Marc Stegger, whose team analyzes genomic data.

Scientists here say granular research only makes sense if the knowledge provides a way to safeguard the country — and it has in the past. A year ago, when the alpha variant was taking hold, Denmark quickly tightened its lockdown, significantly blunting the wave.

The government hasn't implemented a comprehensive lockdown this time. But it has tried to be responsive to the emerging science. Still, the spread has continued apace. For early omicron cases, Denmark tried to quarantine not just close contacts, but contacts of contacts; the strategy was abandoned after nine days because it became untenable.

At the State Serum Institute, many scientists talk wearily about the pre-omicron days as if reflecting on another era, back when the pandemic was manageable and understandable. In the past several weeks alone, the testing lab has hired 100 new people. It bought 20 new PCR machines. It started dipping into its reserve stockpile of plastic lab parts and competing with other countries for supplies. The institute's Christmas party, planned for last week, was canceled.

Scientists say they feel trepidation — and also a bit of awe — about what they are seeing: an incredibly fit virus, winning a turf war against delta. As of Monday — the most recent day with complete, publicly released data — omicron accounted for 26.8 percent of cases. A week earlier, omicron's share had been 4.9 percent.

"It's moving so fast," Cohen said, as more swabs arrived at the lab below his second-floor office. He said his chief concern was to keep things running. He called himself a "lab guy," and said thinking about the bigger picture was for the epidemiologists. But he ventured: "I can't help but have a fatalistic opinion: that we're all going to get this."

For the moment, the full consequences of the omicron variant are still on the horizon — weeks away, on a computer screen, or part of government warnings. In Britain, the only country that can match Denmark's variant surveillance, Prime Minister Boris Johnson has talked about a "tidal wave" of incoming cases. The variant is already dominant in London, and Europe's center for disease control says it is likely to become dominant on the continent as a whole in January or February. The United States, too, is bracing for a big wave and swamped hospitals as early as next month.

But the models project only a few weeks into the future, and what lies beyond — after the omicron wave crests and dissipates — is left to the scientific imagination.

At the State Serum Institute, the man with the imagination is Anders Fomsgaard, one of Denmark's best-known virologists. He's a saxophone enthusiast with curly hair. His colleagues call him an idea man. And he works in a squat yellow building where researchers are growing omicron cultures.

He greeted a visitor at the entrance, under neon lights shaped like geometrical fragments, which he explained represent HIV.

"Another epidemic," he said. "Still going on, by the way."

Perhaps, he said, omicron's origins are connected to HIV, as the virus could have come from an immunocompromised person whose body couldn't kill off the virus, which was able to grow and change. Even in Danish hospitals, he said, there are people who have had the coronavirus for seven or eight months. In Denmark, the changes are being monitored; in most places, they are not.

"This could be one of the ways you create this resistant virus," he said.

His goal, he said, is to help humanity finally get ahead of the coronavirus. And to that end, he's leading all sorts of experiments. Among them is research on a vaccine that targets T cells. Such a vaccine wouldn't protect against infection, but its goal would be to stop sickness. The advantage would be that it targets parts of the coronavirus that don't seem to mutate.

"We are all the time responding," he said. "We're behind. We are five steps behind."

He thinks the next month will be brutal, but after that? It's hard to say. Infected people, and there will be many, could come away with a deepened protection — pushing the coronavirus into something less menacing. But he also said the virus is impossible to eradicate fully. Maybe it could jump into rodents. Then maybe back into humans, re-formed. He described the coronavirus as a "master mutator," and clearly, with vaccination, humans are driving the virus into a corner, where it can either weaken or change.

"It could come out on the other end even weaker," Fomsgaard said. "But that is risky business. It might hit another jackpot mutation."

[Karl Henning]

Spoke again today with my cousin living in South Africa (Johannesburg). No fear-mongering, panic-inducing articles in media of the type we see in Europe and the USA. No lockdown. They just returned from a vacation in Cape Town area: restaurants full, malls full, no Covid Pass. Her son-in-law and granddaughter had omicron: headaches, muscle aches, moderate fever, fatigue, all gone after 10 days of rest, sleep and home treatment.

Looks like the Third World is the place to be right now. 

Glad your loved ones are faring well.

[Florestan]

Glad your loved ones are faring well.

I hope and pray we all GMGers and all our loved ones will eventually emerge safe and sound from this bloody mess.

[Mandryka]

Spoke again today with my cousin living in South Africa (Johannesburg). No fear-mongering, panic-inducing articles in media of the type we see in Europe and the USA. No lockdown. They just returned from a vacation in Cape Town area: restaurants full, malls full, no Covid Pass. Her son-in-law and granddaughter had omicron: headaches, muscle aches, moderate fever, fatigue, all gone after 10 days of rest, sleep and home treatment.

Looks like the Third World is the place to be right now. 

Wouldn't it be ironic if disease induced immunity was more effective against omicron than vaccine induced immunity. So that the African population was safer than the people in developed countries. We will know soon enough, I don't even know if it's even a possibility.

[Florestan]

Wouldn't it be ironic if disease induced immunity was more effective against omicron than vaccine induced immunity.

I for one am convinced that this is indeed the case. 

[prémont]

Highly vaccinated countries thought they were over the worst. Denmark says the pandemic's toughest month is just beginning.

By Chico Harlan
Today at 9:24 a.m. EST

Thanks for this. The quoted virologists here have hinted at something similar during the last week but not that explicit until now.

[T. D.]

Wouldn't it be ironic if disease induced immunity was more effective against omicron than vaccine induced immunity. So that the African population was safer than the people in developed countries. We will know soon enough, I don't even know if it's even a possibility.

This (already - I saw it quoted on Bloomberg today) widely-cited article from Imperial College London says that

...the protection against reinfection by Omicron afforded by past infection may be as low as 19%...Controlling for vaccine status, age, sex, ethnicity, asymptomatic status, region and specimen date, Omicron was associated with a 5.40 (95% CI: 4.38-6.63) fold higher risk of reinfection compared with Delta. To put this into context, in the pre-Omicron era, the UK "SIREN" study of COVID infection in healthcare workers estimated that prior infection afforded 85% protection against a second COVID infection over 6 months. The reinfection risk estimated in the current study suggests this protection has  fallen to 19% (95%CI: 0-27%) against an Omicron infection.

https://www.imperial.ac.uk/news/232698/omicron-largely-evades-immunity-from-past/

[Karl Henning]

Thanks for this. The quoted virologists here have hinted at something similar during the last week but not that explicit until now.

At your service, my friend!

[Florestan]

This (already - I saw it quoted on Bloomberg today) widely-cited article from Imperial College London

Argument from authority.

[Todd]

No fear-mongering, panic-inducing articles in media of the type we see in Europe and the USA.

US press coverage of the pandemic has been unfailingly neutral, even-handed, and purely fact-based. 

[SimonNZ]

Argument from authority.

That wasn't an example of the Argument From Authority fallacy because T.D. wasn't claiming it to be a discussion stooping checkmate that nobody had the right to dissent.

If you want an actual example you could look at your own statements whenever the subject of Communism is touched on and you claim your limited subjective individual experience translates here into unquestionable all encompassing objective facts.

[T. D.]

That wasn't an example of the Argument From Authority fallacy because T.D. wasn't claiming it to be a discussion stopping checkmate that nobody had the right to dissent.

If you want an actual example you could look at your own statements whenever the subject of Communism is touched on and you claim your limited subjective individual experience translates here into unquestionable all encompassing objective facts.

I posted a link to the original academic report, no dilutions or interpretations by media. One would ordinarily assume (though perhaps Internet forums are different?  ) that reasonable semi-intelligent individuals could, if they so desire, read it and make their own inferences.

Golly gee whiz, I'd rather read some anonymous Internet blowhard talking out of his ass...

[Que]

Given the fact that the level of mutations of Omicron in comparison to previous variants is very high, it is hardly surprising that previous infection with older variants doesn't provide much protection against reinfection. But it might still make a difference in the severity of the ilness, they just don't know yet.

I guess "it's just like the flu"...

[Florestan]

I posted a link to the original academic report, no dilutions or interpretations by media. One would ordinarily assume (though perhaps Internet forums are different?  ) that reasonable semi-intelligent individuals could, if they so desire, read it and make their own inferences.

You're right. My comment was stupid. I apologize.

[Que]

Covid: Dutch go into Christmas lockdown over Omicron wave

I'm glad I just had a haircut....

[vers la flamme]

I got the booster on Friday, it was the Moderna. I was expecting to be completely wiped out for days like after I got the first shot (the J&J) about 6 months ago, but it was surprisingly mild. Just a headache and some fatigue. Glad to have these antibodies in my system... God knows what the future will look like covid-wise.

Anyone else get their booster recently? What have your experiences been like?

[Karl Henning]

I got the booster on Friday, it was the Moderna. I was expecting to be completely wiped out for days like after I got the first shot (the J&J) about 6 months ago, but it was surprisingly mild. Just a headache and some fatigue. Glad to have these antibodies in my system... God knows what the future will look like covid-wise.

Anyone else get their booster recently? What have your experiences been like?

Glad you took this one in stride. I got my booster some little while ago.

[Karl Henning]

And: the natural consequence of Omicron Meets the Trumpland Vaccine-Resisters ...

Fauci warns omicron variant will cause record-high coronavirus hospitalizations, deaths in U.S.

By Amy B Wang, Sean Sullivan and Hannah Dreier
Today at 9:47 a.m. EST| Updated today at 11:01 a.m. EST

Anthony S. Fauci, the nation's leading infectious-disease specialist, warned Sunday that the United States is likely to see record numbers of coronavirus cases, hospitalizations and deaths as the omicron variant spreads rapidly.

"Unfortunately, I think that that is going to happen. We are going to see a significant stress in some regions of the country on the hospital system, particularly in those areas where you have a low level of vaccination," Fauci said on CNN's "State of the Union."

He continued to urge the unvaccinated to get their shots and those who have received only two doses of either the Pfizer or Moderna mRNA vaccines to get booster doses. Although vaccines cannot be the only layer of protection against the omicron variant, he said, defeating the pandemic would not be possible without them.

Fauci described omicron as "extraordinary," with a doubling time of two to three days. The variant accounts for 50 percent of coronavirus cases in certain regions of the country, which meant it would almost certainly take over as the dominant variant in the United States, he added.

"It is going to be a tough few weeks, months as we get deeper into the winter," Fauci said.

Fauci conceded that the Biden administration needed to do better about increasing the availability of at-home coronavirus rapid tests, though he stressed that the country was in a much better place than it was a year ago, with 200 million to 500 million tests available per month, many of them free.

"We're going in the right direction," he said. "We really need to flood the system with testing. We need to have tests available for anyone who wants them, particularly when we're in a situation right now where people are going to be gathering."

There are still safe ways for vaccinated people to get together for the holidays, including wearing a mask while traveling, testing beforehand and knowing the vaccination status of everyone present at indoor celebrations, Fauci said on ABC News's "Face the Nation."

"If you do these things, I do believe that you can feel quite comfortable with a family setting," he said. "Nothing is 100 percent risk-free, but I think if you do the things that I just mentioned, you'd actually mitigate that risk enough to feel comfortable about being able to enjoy the holiday."

Fauci said he expected it to be months before antiviral drugs can be mass-produced and available to anyone who needs them. While he did not foresee the kind of lockdowns that were put in place in the early days of the pandemic, Fauci also noted that it would be difficult to keep the virus under control when there remained "about 50 million people in the country who are eligible to be vaccinated who are not vaccinated."

President Biden plans to address the nation Tuesday on the status of the country's fight against the virus, the White House said Saturday.

"Building off his Winter Plan," White House press secretary Jen Psaki wrote on Twitter, Biden will announce "new steps the Administration is taking to help communities in need of assistance, while also issuing a stark warning of what the winter will look like for Americans that choose to remain unvaccinated."

Psaki said, "We are prepared for the rising case levels," adding that Biden "will detail how we will respond to this challenge. He will remind Americans that they can protect themselves from severe illness from COVID-19 by getting vaccinated and getting their booster shot when they are eligible."

The speech, coming just before Christmas and New Year's Day, underlines Biden's struggle to contain the pandemic nearly a year into office. On top of the emergence of new variants and attendant challenges, administration has at times faced criticism for what some have described as mixed signals.

Biden won high marks from the public during the first half of the year as cases declined, the country opened up from lockdown and vaccines became widely available. But the past few months have been far more difficult. After he gave a speech on July 4 saying the country was "closer than ever to declaring our independence from a deadly virus," the situation started changing. Case rates increased as the delta variant took a foothold and many Americans refused to get vaccinated.

Now, as closures and new public health precautions are imposed in areas hit hardest by the virus, Biden faces another potentially brutal stretch in the coming weeks that could strain hospitals and schools and further frustrate Americans at a time when many hoped to enjoy the holidays and put the toughest days of the pandemic behind them.