Coronavirus thread

[Pohjolas Daughter]

There's some emerging data to suggest that VE over time of booster shots declines at pretty much the same rate as it does for "full vaccination" with two shots, although with a longer plateau of initial effectiveness. VE seems higher for mRNA vaccines than inactivated virus vaccines, but I haven't yet seen a comprehensive meta-analysis for statistical significance.

The cause is presumably immune escape over time. My gut reaction to this is that mRNA vaccines are not entirely the game changer they were advertised as, at least in this context, and yearly or six-monthly shots will likely be required for the foreseeable future with the continual possibility (which has not yet eventuated) that, as long as the contents of the mRNA "container" remain unchanged, there's the possibility of vaccine-resistant strains emerging. Under those conditions I feel somewhat less inclined to get a booster shot until I see companies start tailoring them to conditions on the ground now, rather than conditions on the ground in March 2020. That said I have another two months until I'm eligible anyway and will wait to see what other data emerge.

Personally speaking I developed symptoms of COVID-19 on Friday (possibly contracting it sometime last week), which I was told was likely Omicron variant based on local seroprevalence; the symptoms match up fairly well (muscle aches/pains, sore throat, cough, etc.). For me it's indistinguishable from the mild cold that would be caused by any other coronavirus at this time of year, but I'm not in any of the at-risk groups (older adults, males, overweight people—or for Omicron specifically, infants). This hasn't really disrupted my routine, since I already worked from home and the symptoms do not prevent me from being mobile and active—in fact I'm walking more than usual, just due to the fact that I can't run errands outside anymore (no grocery shopping, no public transit, etc.) but get stir crazy at home.

This doesn't prove Omicron is a "mild" variant; I know a number of other people who've had it and who were also not strongly affected, but people I know tend to skew younger and healthier. And yes, this is a breakthrough infection, but I likely wouldn't have contracted it at all in most circumstances; however, since moving back to New York my diet has been severely disrupted, so my health hasn't been as good in general. That is an untestable hypothesis obviously, but hyperglycaemia is known to correlate with increased rate of COVID-19 infection, severity of COVID-19 illness, and death from or exacerbated by COVID-19, and hyperglycaemia can be a result of a high-calorie diet. My blood sugar levels are in the normal range, but it's not out of the question that consuming mostly processed/prepared foods and energy drinks for several months might have made me more vulnerable.

The immune response to this variant does not seem to confer long-term immunity—though we obviously don't have long-term population-scale data, only statistical models—so I won't be too surprised if I catch it again at some point.

I'm very sorry to hear of your health issues.  Can you get tested anywhere and soon? Or possibly getting ahold of a kit and doing it initially yourself?

May I ask how you ended up eating a high-processed food route?  What changed?  Were there no grocery stores/farmers markets nearby?  Or changes in your home/relationship?  Or issues with food deliveries due to Covid?  Just trying to understand.

Hope that you don't have it and all goes well--truly,

PD

[Mandryka]

There's some emerging data to suggest that VE over time of booster shots declines at pretty much the same rate as it does for "full vaccination" with two shots, although with a longer plateau of initial effectiveness. VE seems higher for mRNA vaccines than inactivated virus vaccines, but I haven't yet seen a comprehensive meta-analysis for statistical significance.

The cause is presumably immune escape over time. My gut reaction to this is that mRNA vaccines are not entirely the game changer they were advertised as, at least in this context, and yearly or six-monthly shots will likely be required for the foreseeable future with the continual possibility (which has not yet eventuated) that, as long as the contents of the mRNA "container" remain unchanged, there's the possibility of vaccine-resistant strains emerging. Under those conditions I feel somewhat less inclined to get a booster shot until I see companies start tailoring them to conditions on the ground now, rather than conditions on the ground in March 2020. That said I have another two months until I'm eligible anyway and will wait to see what other data emerge.

Personally speaking I developed symptoms of COVID-19 on Friday (possibly contracting it sometime last week), which I was told was likely Omicron variant based on local seroprevalence; the symptoms match up fairly well (muscle aches/pains, sore throat, cough, etc.). For me it's indistinguishable from the mild cold that would be caused by any other coronavirus at this time of year, but I'm not in any of the at-risk groups (older adults, males, overweight people—or for Omicron specifically, infants). This hasn't really disrupted my routine, since I already worked from home and the symptoms do not prevent me from being mobile and active—in fact I'm walking more than usual, just due to the fact that I can't run errands outside anymore (no grocery shopping, no public transit, etc.) but get stir crazy at home.

This doesn't prove Omicron is a "mild" variant; I know a number of other people who've had it and who were also not strongly affected, but people I know tend to skew younger and healthier. And yes, this is a breakthrough infection, but I likely wouldn't have contracted it at all in most circumstances; however, since moving back to New York my diet has been severely disrupted, so my health hasn't been as good in general. That is an untestable hypothesis obviously, but hyperglycaemia is known to correlate with increased rate of COVID-19 infection, severity of COVID-19 illness, and death from or exacerbated by COVID-19, and hyperglycaemia can be a result of a high-calorie diet. My blood sugar levels are in the normal range, but it's not out of the question that consuming mostly processed/prepared foods and energy drinks for several months might have made me more vulnerable.

The immune response to this variant does not seem to confer long-term immunity—though we obviously don't have long-term population-scale data, only statistical models—so I won't be too surprised if I catch it again at some point.

Look after yourself obvs. Sounds like you need the Jewish penicillin, a nice plate of chicken soup.

(All these people with mild cold like symptoms being asked to self isolate in Winter. What on earth is going to happen?!)

[amw]

I'm very sorry to hear of your health issues.  Can you get tested anywhere and soon?

NYC has free test sites all over the city—that's how I found out in the first place (would have otherwise dismissed this as the usual seasonal cold). It's a 1-6 hour wait at this point due to the surge, though. There's also a company that offers at-home testing, but it's similarly spotty; after I tested positive we booked at-home tests for the two of us (I live with my brother at the moment) for three separate times and only once did anyone show up with testing kits. Luckily my brother did test negative but his exposure means he's not able to visit his girlfriend for the holidays, due to the risk of becoming symptomatic down the line. False negative results for asymptomatic infectees is apparently a known issue for the Omicron variant in particular.

May I ask how you ended up eating a high-processed food route?  What changed?  Were there no grocery stores/farmers markets nearby?  Or changes in your home/relationship?  Or issues with food deliveries due to Covid?  Just trying to understand.

There's a variety of reasons. There were many factors resulting in a lack of motivation to cook or prepare food (mostly related to mental health, housing situations, or stress), and a few factors resulting in a lack of desire to consume food (a caffeine addiction developed as a way to transition into the workforce; pandemic-related weight gain).

Look after yourself obvs. Sounds like you need the Jewish penicillin, a nice plate of chicken soup.

That was my mom's recommendation, of course. Also something about bone broth.

People aren't really isolating even if they are coughing or sneezing; every time I go out for walks the streets are as crowded as ever, at least in this part of town. Of course that probably accounts for some of why the city has 22,000+ new cases each day. I doubt people will take this variant seriously here until death rates become significant, and given the vaccination & seroprevalence rates here that may not ever happen. (People would also take it seriously if a lockdown was instituted, even a partial one, but that presumably won't happen until after the holidays if at all.)

[Todd]

My gut reaction to this is that mRNA vaccines are not entirely the game changer they were advertised as

I think that is a safe thing to say. 

I hope you feel better soon, and if you do have Covid, whatever the variant, that is passes quickly. 

[Holden]

Queensland has almost hit the 90% vax mark and because of this decided to open up its borders on Dec 17. The new CHO is an immunologist and has adopted a very different approach to his predeccessor. He understands that herd immunity can exist, especially with the weaker omicron strain and now is the time to move forward. This is what he had to say:

That came after a similar record just the day before with 186 cases, with state Chief Health Officer John Gerrard earlier in the week saying case numbers would grow exponentially.

He went even further on Thursday, pointing out that COVID-19 was going to go right through Queensland, almost certainly in the form of the Omicron variant, and that authorities were not only not trying to stop it, they were counting on it.

"Not only is the spread of this virus inevitable, it is necessary," Dr Gerrard said.

"In order for us to go from the pandemic phase to an endemic phase, the virus has to be widespread. We all have to have immunity."

There are a number of historical precedences for this approach. The obvious one is the 'Spanish Flu' of 1918-21. This flu's strain was a novel one and is an H1N1 variant and as the '1s' in it's name suggests it was, like Covid19, a brand new Flu variant which we had not seen before and therefore had no natural immunity to. Of course it affected much of the worlds population (9000 alone died here in Australia). This flu mutated constantly over the next three or so years and eventually became much milder and endemic as a result. All this without a vaccine suggesting that people built up an immunity. Today, unless you have compromised health, if you get H1N1, your chances of survival are very high because herd immunity has worked. Yearly vaccinations are also useful but the first H1N1 flu vaccine didn't appear until 1938.

It's probable that even if we didn't have Covid vaccines that exactly the same would have happened today and the appearance of the omicron strain appears to support this fact. Another point of interest is that the 'Spanish Flu' pandemic affected young people more than than those who were older and attacking the most healthy in our population speeded up the immunity process as a large majority of those who died had health issues, many of them socio-economically induced. Those included years of poor diet, lack of access to medical facilities, etc. The healthy tended to survive and it was them that contributed to the immune process.

So, unless you are an anti vaxxer, take some comfort in the fact that if you are healthy are vaxxed and have no comorbidities then you are probably safe.

[Spotted Horses]

Personally speaking I developed symptoms of COVID-19 on Friday (possibly contracting it sometime last week), which I was told was likely Omicron variant based on local seroprevalence; the symptoms match up fairly well (muscle aches/pains, sore throat, cough, etc.). For me it's indistinguishable from the mild cold that would be caused by any other coronavirus at this time of year, but I'm not in any of the at-risk groups (older adults, males, overweight people—or for Omicron specifically, infants). This hasn't really disrupted my routine, since I already worked from home and the symptoms do not prevent me from being mobile and active—in fact I'm walking more than usual, just due to the fact that I can't run errands outside anymore (no grocery shopping, no public transit, etc.) but get stir crazy at home.

Sorry to hear you have apparently been affected. I hope your symptoms continue to be mild and that you have a rapid recovery.

[Pohjolas Daughter]

I went into a local CVS store yesterday and noticed that they had several large signs up saying that they didn't have any of the Covid test kits.  I'm guessing that a lot of people bought them with holiday plans in mind?  Or are some folks just buying them to have on hand should they start to feel unwell?  Or were around someone who had tested positive?  Or all of the above? 

Are folks here trying to get ahold of kits?

PD

[MusicTurner]

They're very popular and usually sold out here, prices typically 5-8 Euros. There are some options via websites, and a delay in delivering + a handling fee. In the provinces, where test centres can be far away, and among busy families with children, they're of particularly good use, of course. I considered buying some a week ago, but they sold out too quickly. Yet public quick test facilities are just a small bike tour or metro ride away, and free, though there's a good deal of queueing/crowds obviously - my three quick tests this week implied about 45 mins - 45 mins - 15 mins of waiting. As for PCRs, they're upscaling capacity, in a week or so. But if I see the tests for sale here, I'll probably be getting at least one, as a reserve  ...

[Pohjolas Daughter]

They're very popular and usually sold out here, prices typically 5-8 Euros. There are some options via websites, and a delay in delivering + a handling fee. In the provinces, where test centres can be far away, and among busy families with children, they're of particularly good use, of course. I considered buying some a week ago, but they sold out too quickly. Yet public quick test facilities are just a small bike tour or metro ride away, and free, though there's a good deal of queueing/crowds obviously - my three quick tests this week implied about 45 mins - 45 mins - 15 mins of waiting. As for PCRs, they're upscaling capacity, in a week or so. But if I see the tests for sale here, I'll probably be getting at least one, as a reserve  ...

Probably not a bad idea to get one.  Are the kits all one-test-only?

PD

[Szykneij]

Probably not a bad idea to get one.  Are the kits all one-test-only?

PD

The kits we got have two tests in each. Last week, I had no problem finding them at the local CVS and my wife got some next day through Amazon. This week, everyone is all sold out and Amazon won't have them to ship until at least mid-January. I believe it's the combination of the holidays as well as growing concern over increasing numbers of cases.

[Pohjolas Daughter]

The kits we got have two tests in each. Last week, I had no problem finding them at the local CVS and my wife got some next day through Amazon. This week, everyone is all sold out and Amazon won't have them to ship until at least mid-January. I believe it's the combination of the holidays as well as growing concern over increasing numbers of cases.

Glad that you were able to get some.  I did a bit of quick googling at my end to see where there are and/or will be free testing sites near me.  There are some in local towns and there should be one opening up quite close to me within a few weeks.  I suspect that if worse comes to worse, that I could probably be tested at my local hospital.

I've been checking occasionally on what's been going on in the lead up to the Australian Open (Yes, I know, I know:  I love my tennis!).  Ben Rothenberg posted on Twitter what the rules were that the Australian Open would be operating under in terms of medical exemptions from having received Covid vaccine shots.  They are really strict.  Note:  if a player wishes to apply for a ME, they must do so anonymously.  One of the biggest questions being:  will Novak Djokovic be there?  He has been mum about his vaccination status. It's a bit confusing keeping up with all of the news.  Here are the exemption rules:

https://twitter.com/BenRothenberg/status/1473710660794126345

PD

[Que]

Omicron: Good news, bad news and what it all means

Omicron is less severe
If you catch Omicron then you are less likely to become seriously ill than with previous variants.
Studies from around the world are painting a consistent picture that Omicron is milder than the Delta variant, with a 30% to 70% lower chance of people infected ending up in hospital. Omicron can cause cold-level symptoms such as a sore throat, runny nose and a headache, but that does not mean it will be mild for everyone and some will still be seriously ill.

Changes to the virus seem to have made it less dangerous, but most of the reduced severity is down to immunity as a result of vaccination and previous bouts of Covid.

So, what I get from that is that for the unvaccinated that haven't been infected before, Omicron might be a real threat. Because they are going to catch it, for sure.

BTW I'm surprised that some still keep telling us that viruses have a natural tendency to become more benign. This is a completely bogus assumption since it confuses the phenomenon of mutation (which is completely random), the process of natural selection (which is dependent on the survival rate, for a virus the level of infectiousness and availability of suitable hosts) and the effect of immunisation.

[Mandryka]

Omicron: Good news, bad news and what it all means

Omicron is less severe
If you catch Omicron then you are less likely to become seriously ill than with previous variants.
Studies from around the world are painting a consistent picture that Omicron is milder than the Delta variant, with a 30% to 70% lower chance of people infected ending up in hospital. Omicron can cause cold-level symptoms such as a sore throat, runny nose and a headache, but that does not mean it will be mild for everyone and some will still be seriously ill.

Changes to the virus seem to have made it less dangerous, but most of the reduced severity is down to immunity as a result of vaccination and previous bouts of Covid.

So, what I get from that is that for the unvaccinated that haven't been infected before, Omicron might be a real threat. Because they are going to catch it, for sure.

Also note that the effect of omicron on older cohorts is not clear at all. Omicron seems to be able to break through vaccine protection against symptoms more easily than delta, and so it is possible that there will be more symptomatic cases amongst older people than there were before. And even if omicron produces less severe disease than delta in general, paradoxically those older cohorts could find themselves in hospital more than they did with delta, because of their vulnerability and because of omicron's ability to cause breakthrough symptoms.

Everything is still shrouded in uncertainty.

(Sorry, gobbledygook again.)

[Karl Henning]

The town of Danvers (where I serve as choir director) has instituted a mask mandate. This doesn't change anything for our Lessons & Carols, as we have been singing masked all this while.

Nice to read this on Christmas Eve:

Denmark sees initial signs that dire omicron surge can be avoided

By Chico Harlan
Today at 11:19 a.m. EST

Early benchmarks from Denmark on infections and hospitalizations are providing grounds for guarded optimism that highly vaccinated countries might be able to weather the omicron wave.

The developments, coupled with Denmark's speedy rollout of booster shots, have raised hopes the country can avoid the dire surge for which it has been bracing.

"It's too early to relax, but it's encouraging that we are not following the worst-case scenario," said Tyra Grove Krause, the chief epidemiologist at Denmark's State Serum Institute.

Denmark's detailed, nationwide program for coronavirus testing and analysis gives its scientists a trove of real-time data about the pandemic. Because of that — and because it was one of the first countries outside of Africa to witness omicron's explosive potential — it has turned into a European bellwether for what to expect with the omicron variant.

Over the last week, the country has fared better than it was expecting. After surging to record-breaking levels, the number of daily cases has stabilized. Officials recorded 12,500 cases on Thursday, compared to 11,000 late last week.

More important, hospitalizations have come in — so far — on the very low end of what was projected. A week ago, Denmark's government science institute said daily new coronavirus hospital admissions could range between 120 and 250 patients by Christmas Eve. In recent days, daily admissions have hung around 125.

"That is quite promising," Grove Krause said.

The early signals from Denmark don't provide any direct measure on the severity of the variant, one of the key questions in this phase of the pandemic. But they track with other emerging data and studies from Britain and South Africa that suggest omicron is less likely to lead to hospitalization than the delta variant.

Scientists caution that there are still many uncertainties, and that even if omicron is less likely to cause hospitalization, its increased transmissibility means countless sicknesses and disruptions. The virus could also spread so widely that it nonetheless leads to an influx at hospitals.

Concerns remain about the health system in Denmark, Grove Krause said, because omicron infections are disproportionately concentrated among the young. For now, Grove Krause said, temporary school closures and social precautions have helped slow the spread — but the country could see a spike after holiday gatherings that bring together the young and old.

Even as cases have slowed, there are other signs of omicron's potential to cause chaos. Over the last two weeks, the number of cases among health care workers has more than doubled. A weekly government monitoring report said there had been two omicron outbreaks in nursing homes.

Since omicron emerged in November, scientists have been racing to understand its implications and make sense of a variant that's moving far more quickly than its predecessors.

A few data points emerged this week, with one Scottish study suggesting the risk of hospitalization was almost 60 percent less with omicron than delta. Another analysis, conducted by Imperial College London, said people with omicron cases were 20 percent less likely to go the hospital and 40 percent less likely to be hospitalized overnight. And South Africa, the epicenter of the first apparent outbreak, has seen much lower hospitalization rates than in other waves.

It remains unclear whether trends from South Africa — where demographics skew younger — will play out in other parts of the world. It's also unclear whether and to what extent omicron's reduced severity is a feature of the virus itself, or rather a sign of population-level immunity stemming from vaccinations and prior infections.

Compared to delta, omicron is far better at evading vaccines and causing infections in those who have been inoculated. But Denmark's experience shows that a rapid booster rollout might be able to help cut down rising infection numbers. A team of scientists at the State Serum Institute said in a research paper this week that Pfizer-BioNTech booster shots appeared to provide a 55 percent protection against infections, compared to cases in those who had received two doses.

Even if that level of protection dips over time, boosters "can help us through the next months," Grove Krause said.

According to Our World in Data, Denmark has issued the most per capita booster shots of any European Union country. Denmark said in its latest monitoring report, released Thursday, that 36.8 percent of its population had been boosted, more than double the level from two weeks earlier. Overall, 77.2 percent of the country's population has received at least two doses.

[amw]

BTW I'm surprised that some still keep telling us that viruses have a natural tendency to become more benign. This is a completely bogus assumption since it confuses the phenomenon of mutation (which is completely random), the process of natural selection (which is dependent on the survival rate, for a virus the level of infectiousness and availability of suitable hosts) and the effect of immunisation.

It's rather a misunderstanding. Viruses tend to become more transmissible and less deadly over time, because this is an almost inevitable result of natural selection due to how viruses reproduce; mutations that allow hosts to spread virions more widely and more quickly are likely to outcompete others. (This does not necessarily mean that viruses have to leave their hosts alive and healthy to gain advantages; mutations that grant a virus greater ease of dispersion among hosts, e.g., changing from droplet transmission to aerosol transmission, can be just as effective. But less common.)

Assuming that this makes more transmissible–less deadly viruses benign or harmless is due to people taking Margaret Thatcher too literally. In a population of one million people, assuming completely unchecked spread, a viral strain that infects 5% of the population and has a 10% case fatality rate will cause 5,000 deaths*, exactly the same as a viral strain that infects 25% of the population and has a 2% case fatality rate; but in the latter case, the number of sick—not dead—people likely to require various medical services and (potentially) having to be quarantined will be five times higher. The second scenario thus has a significantly more disruptive effect on society and human life even though any single individual's chance of dying from the virus is five times lower. Human beings, no matter how many quarantine rooms you distribute them into, or how many masks, face shields, etc. you distribute to create barriers between them, are interdependent.

As such, there is no particular reason to treat a more transmissible variant as "good news", or to assume that viruses will eventually evolve to become completely harmless, and even a viral variant that carries an exceptionally low risk of death may still be very dangerous if it is also exceptionally transmissible—especially considering that the frequency of disabling longterm post-viral illnesses has significantly increased over the past five to seven decades and does not appear to correlate strongly with the severity of the viral disease, and these illnesses remain almost entirely unstudied, unaddressed, and disbelieved in by doctors despite this vast increase due to a combination of social factors (medical biases: women being more affected, overweight and sedentary people being more affected, lower-income people being more affected; systemic economic issues: there is no profit motive in studying "new" or "increasingly prevalent" illnesses unless they pose risks of large-scale market volatility or, like cancers, cause death in almost all cases).

* (not really, but simplified here for ease of understanding the arithmetic)

[Karl Henning]

Peter Bailey-Wells, Ryan Huddle, Daigo Fujiwara and Amanda Kaufman Globe Staff:

Massachusetts on Friday reported 10,040 new confirmed coronavirus cases, the highest total reported in a single day since the start of the pandemic. It was the third day in a row that the state reported a new single-day high.

The state also reported 32 new confirmed coronavirus deaths and 42,569 vaccinations, including booster shots, had been administered, the Department of Public Health said.

The state also reported that 1,632 patients with COVID-19 were in the hospital. On Friday, the seven-day percent positivity was 8.32 percent.

[Karl Henning]

What vaccination rate does Mass. have?

Higher than the US average.

[drogulus]

Higher than the US average.

     The most vaxed are:


Vermont   479,602   77%
Puerto Rico   2,448,200   77%
Guam   126,582   76%
Rhode Island   804,503   76%
Maine   1,014,290   75%
Connecticut   2,649,289   74%
Massachusetts   5,114,904   74%

[Karl Henning]

Hong Kong is clinging to 'zero covid' and extreme quarantine. Talent is leaving in droves.

[Karl Henning]

Coronavirus detected in Boston-area waste water soars to new record levels

By Maria Elena Little Endara Globe Correspondent,Updated December 27, 2021, 1 hour ago

The detection of coronavirus in Boston-area waste water has reached record-breaking levels, with the most recent seven-day average soaring past previous record highs set earlier this month.

On Dec. 23, the seven-day average of virus traces in the waste water in the southern sample of the Massachusetts Water Resources Authority's territory was 2,574 RNA copies/mL. That's up from 1,136 copies/mL on Dec. 1, meaning the average has increased by 127 percent in the last three weeks.

Waste water testing serves as an early warning sign for a coming COVID-19 surge. Cambridge-based Biobot Analytics, which tests the waste water coming into MWRA's Deer Island treatment plant, has said it has found that the amount of virus in the waste water is correlated with newly diagnosed coronavirus cases four to 10 days later.

The increase in the waste water levels continues a trend that began around late November, but the tests found that the seven-day averages of virus traces in the waste water have risen incredibly fast over the last three weeks.

In the northern sample, which includes the Boston area, the seven-day average rose from 1,328 RNA copies/mL on Dec. 16 to 2,411 copies on Dec. 23, meaning that the average has almost doubled in the last seven days.

Levels of coronavirus in waste water coming from the northern and southern samples of the MWRA's territory have both risen substantially, well beyond levels seen at the height of the deadly winter surge in mid-January 2021, when cases rose to 5,000-plus per day.

In the past several weeks, Massachusetts has seen a spike in COVID-19 cases. On Dec. 24, the state reported 10,040 new confirmed cases, the highest total reported in a single day since the start of the pandemic. It was the third day in a row that the state reported a new single-day high.

Earlier last week, Governor Charlie Baker deployed the National Guard to help hospitals in Massachusetts struggling with staff shortages and ordered them to cancel nonessential surgeries to accommodate a tide of patients sick with COVID and other serious illnesses.