The Corona Pandemic

Yeah, I think we are fucked here, and yet I see and hear the ‘it is supposedly mild’ claim all the time. Our ICUs are sloping upward significantly, nothing like the proportions of previous waves - but our case load is 5x any prior wave with positivity 3x previous highs and significant new restrictions on testing eligibility. One out of every 6 cases since March 2020 is infectious today. Even reported cases are almost 3x what they were 10 days ago, and when that smaller percentage hits that larger denominator, we will see unsustainable numbers

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Yeah I agree, we are by no means out of the woods. But the first signs, at least here in Switzerland, seem to indicate that the case vs. hospitalisation rate is significantly lower with the new variant than it was with delta. Despite of new number of cases going through the roof (around double of our previous record numbers last winter), the hospitalisation rate is going down significantly. That makes me reasonably optimistic for the coming times.

Of course, if we go from 20k new cases to 200k new cases a day, we’ll have a catastrophe on our hands. There is very much a relationship between new cases and hospitalisation.

I don’t really know the situation for other countries, but in our case, if we can maintain the current infection rate, we should be good. Time will tell.

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Ontario is back to virtual schools, closed rec facilities, indoor dining shut (-20 C today, but outdoor dining allowed :rofl:). Capacity limits to 50% on businesses. Basically our step 2 lockdown.

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We tend to think when people are infected they have just one genetically identical version of the virus. In reality every infected person has a population.

Roughly an infected person at peak, has 100 billion virus particles. Every time the virus replicates there is the potential for error (random mutations in one of the 30,000 nucleotides). Most of these mutations offer no advantage sometimes disadvantages. This COVID viral population (within a single person) is effectively in a race against one another. Those who start the race late have little chance of winning, those who don’t replicate as quickly or avoid the immune system as well , are also likely to lose the race. If you catch another variant (alpha/beta/delta/ omicron) half way through, they just enter the race a bit later.

These are the primary selective pressures that drive evolution. But if your not as good at inter-host transmission you ultimately win the battle (within the host) but lose the war (replicating quickly to be able to infect other hosts).

Vast majority of time these random mutations offer no meaningful advantage are used in New Zealand for contract tracing. By doing whole genome sequencing we know person one had say delta with mutations ABCD, he must have infected person two who has ABCDE. That different to person three also with delta who has mutations ABXYZ. Person three likely must have caught it from someone else

The thing is you can have mutations ABCD and this makes no meaningful difference to the virus. Mutation E is not noteworthy either. But together ABCDE could be the new variant Pi.

This graphic is pretty cool. It shows the mutations in the spike protein. Although there is commonality it’s not a simple evolution of alpha to beta to delta to omicron.

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Evidence is really mounting that populations with extensive previous infection can get through this reasonably well, with a fairly low hospitalization and a lower degree of intensity to those hospitalization cases. Places where that isn’t the case are going to be in more trouble, even though that broadly holds true.

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So the countries with zero covid strategy might be punished later down the line? I wonder what this means for China for instance…

Goddamn. Not really a surprise, but a study suggesting this variant might even have spread faster than measles.

https://onlinelibrary.wiley.com/doi/abs/10.1002/jmv.27560

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Apparently over a million new cases in the US yesterday. Majority already Omicron.

Well, zero covid plus low vaccination would mean they would get very hard this time round. Still probably better off, given that the death rate from Omicron even in unvaccinated populations is lower than prior variants, but the toll would still be terrible.

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reading between the lines here…

Appears that we have reached that point where the virus is burning itself out. similarly to the A/H1N1 influenza strain that wiped out 50,000,000 people a hundred years ago with the “spanish flu”, history is repeating itself.

I was doing some reading up on it a few days back, and it’s interesting the censorship that was happening even then in the mainstream news…

on a lighter note:

image

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I think the ‘burnout’ scenario is a distinct possibility, maybe even the most likely now. But I actually think the end of the Spanish flu was more complex than that. The waves in covid have been directly attributable to different variants, whereas with Spanish flu that is a theory, but despite efforts, not much evidence has been found to support that. The waves were as likely to be a function of slower communications/transport producing a reverb effect as immune response faded.

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And this despite one of the largest states in the country, one in which mitigation measures are fairly absent, has really limited testing available. People who need tests are simply going without.

A friend of mine has been exposed to a case and has spent 2 days looking for a test and cannot find one. The city/county have set up some testing sites, but they dont have the resources as it is normally the state who is responsible for responding to situations like this and we have not a single state operated/funded testing site. That means, within the city we have only 2 city/county run facilities, but they are both first come first serve, with lines that stretch back a mile as early as 5am despite them not opening until 9am, and so typically have exhausted their resources by midday. This means potentially sitting in your car for 5+ hours only to eventually be told to come back tomorrow. There are commercial sites available but those are all fully booked for days. This guy is on anti-rejection meds after having had a liver transplant and so is immunocompromised, so is a candidate for the very limited supply of monoclonal antibody treatment early in his infection. This is what the governor keeps stressing - “early treatment saves lives” - but early treatment requires the ability to get a test, and they are just damn impossible to get.

Omicron is already overrunning Delta in Canada as well, am sure Arminius has already posted the stats.

Testing capacity is also overwhelmed here, so those who are stick are simply just staying home over the holidays. Schools are out for another week in the interim here in BC so I get to work from home…

I’m hoping this fizzles out in time for Spring, but they’ve only closed nightclubs and limited capacity at a number of businesses. took my son to swimming lessons yesterday, the public pool was open for business.

Jr got his first shot two weeks ago.

Absolutely.

Test availability is shocking.

There is still hardly any mask wearing or acknowledgement of the situation in the parts of the US I’ve been visiting. We have been stared at like mad people for wearing masks in public places.

I’m not sure how serious it would have to get before people changed their behaviour.

I have relatives wintering in Florida who were planning to come back to Canada in mid-December, but decided not to given the state of cases in Canada, plus the risks involved in air travel. I am now seriously wondering what a wave like this will look like in Florida. Ontario government response has been inept, but has not been outright denial. It might be time for them to drive home.

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Our underlying rate of new cases in Ontario must be over 100k a day now, given ~18k/day positive but 30% positivity with extreme restrictions on who can actually get PCR tests. No virus, no matter how infectious, can sustain that rate for that long. between exposures that lead to antibody response and infections, it will be through the population in a matter of weeks and start the ‘burn out’ phase.

Anecdotally, the current wave is much more immediate to me. I know of so many proximate cases, or likely cases. An employee who dropped by cheques for signature last week let me know he tested positive yesterday. Both masked, just handed over a folder outdoors, then reversed the process when signed, but ‘fleeting encounter’.

We’re already seeing over twice the daily case load as we saw at the peak of the summer wave with Delta, and this is despite ongoing limitations with testing. We can also assume that real numbers for both peaks are really much higher than reported given the long standing data reporting fuckery employed at Tallahassee.

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