The COVID-19 pandemic

[jeffster]

I removed Porcupine from this lists, due to their small population. Here is the 7-day unadjusted average per 100k.

• Region of Waterloo Public Health and Emergency Services 53.4
• Peel Public Health 48.4
• City of Hamilton Public Health Services 42.7
• Brant County Health Unit 36.1
• Thunder Bay District Health Unit 34.7
• Durham Region Health Department 34.0
• Niagara Region Public Health 33.9
• Toronto Public Health 32.6
• Haliburton, Kawartha, Pine Ridge District Health Unit 26.5
• Lambton Public Health 26.0

Hopefully now that we're #1 in Ontario, we can get more help. Under the old scheme, Waterloo Region, Hamilton and Peel would still be "Red". Peel is still heading in the right direction, and Hamilton is slowly getting there.

I did hear through the grapevine that RoW might be the only area not going to Stage 2 if our numbers don't improve. Not sure how valid that grapevine information is though.

[kps]

https://news.ontario.ca/en/release/10003...-hot-spots

We're now officially a hot spot and those who got mRNA'd by May 9 (i.e. high priority) are eligible for second doses next week.

[tomh009]

I did hear through the grapevine that RoW might be the only area not going to Stage 2 if our numbers don't improve. Not sure how valid that grapevine information is though.

The entire province is moving in lockstep. They determined that the different rules in different regions created more problems than they solved.

[tomh009]

THURSDAY 2021-06-10

Waterloo Region reported 62 new cases for today (17.5% of the active cases) and one more for yesterday for 55; 332 new cases for the week (+16 from yesterday, +68 from last week), averaging 13.6% of active cases. 392 active cases, +71 in the last seven days.

7,072 vaccinations with a seven-day average of 6,825. 55.47% of the total regional population (+0.55%) has at least one dose of vaccine, and 5.90% (+0.58%) has been fully vaccinated.

Ontario reported 590 new cases today with a seven-day average of 617 (-40). 939 recoveries and 11 deaths translated to a decrease of 360 active cases and a new total of 6,464. -3,497 active cases for the week and 130 deaths (19 per day). 31,429 tests with a positivity rate of 1.88%. The positivity rate is averaging 2.54% for the past seven days, compared to 3.35% for the preceding seven.

New case variants reported today (these are substantially delayed so they do not match the new case numbers):

• Alpha (B.1.1.7): 1509
  
• Beta (B.1.351): 3
  
• Gamma (P.1): 25
  

450 patients in ICU (-16 today, -96 for the week) and 516 total hospital patients (-213 for the week).

182,350 doses of vaccine administered, with a seven-day average at 162,066 (previous week was 137,472). 62.69% of total provincial population vaccinated (+0.45% from yesterday), 9.51% fully vaccinated (+0.80% from yesterday).

• 61 cases in Waterloo: 9.9 per 100K (based on provincial reporting)
  
• 130 cases in Peel: 9.4 per 100K
  
• 9 cases in Brant: 6.6 per 100K
  
• 38 cases in Hamilton: 6.6 per 100K
  
• 26 cases in Niagara: 5.8 per 100K
  
• 23 cases in Middlesex-London: 5.7 per 100K
  
• 114 cases in Toronto: 3.9 per 100K
  
• 5 cases in Thunder Bay: 3.3 per 100K
  
• 21 cases in Durham: 3.3 per 100K
  
• 17 cases in Halton: 3.1 per 100K
  
• 16 cases in Simcoe-Muskoka: 3.0 per 100K
  
• 32 cases in York: 2.9 per 100K
  
• 25 cases in Ottawa: 2.5 per 100K
  
• 6 cases in Wellington-Dufferin-Guelph: 2.2 per 100K
  

[danbrotherston]

THURSDAY 2021-06-10

Waterloo Region reported 62 new cases for today (17.5% of the active cases) and one more for yesterday for 55; 332 new cases for the week (+16 from yesterday, +68 from last week), averaging 13.6% of active cases. 392 active cases, +71 in the last seven days.

7,072 vaccinations with a seven-day average of 6,825. 55.47% of the total regional population (+0.55%) has at least one dose of vaccine, and 5.90% (+0.58%) has been fully vaccinated.

Ontario reported 590 new cases today with a seven-day average of 617 (-40). 939 recoveries and 11 deaths translated to a decrease of 360 active cases and a new total of 6,464. -3,497 active cases for the week and 130 deaths (19 per day). 31,429 tests with a positivity rate of 1.88%. The positivity rate is averaging 2.54% for the past seven days, compared to 3.35% for the preceding seven.

New case variants reported today (these are substantially delayed so they do not match the new case numbers):

• Alpha (B.1.1.7): 1509
  
• Beta (B.1.351): 3
  
• Gamma (P.1): 25
  

450 patients in ICU (-16 today, -96 for the week) and 516 total hospital patients (-213 for the week).

182,350 doses of vaccine administered, with a seven-day average at 162,066 (previous week was 137,472). 62.69% of total provincial population vaccinated (+0.45% from yesterday), 9.51% fully vaccinated (+0.80% from yesterday).

• 61 cases in Waterloo: 9.9 per 100K (based on provincial reporting)
  
• 130 cases in Peel: 9.4 per 100K
  
• 9 cases in Brant: 6.6 per 100K
  
• 38 cases in Hamilton: 6.6 per 100K
  
• 26 cases in Niagara: 5.8 per 100K
  
• 23 cases in Middlesex-London: 5.7 per 100K
  
• 114 cases in Toronto: 3.9 per 100K
  
• 5 cases in Thunder Bay: 3.3 per 100K
  
• 21 cases in Durham: 3.3 per 100K
  
• 17 cases in Halton: 3.1 per 100K
  
• 16 cases in Simcoe-Muskoka: 3.0 per 100K
  
• 32 cases in York: 2.9 per 100K
  
• 25 cases in Ottawa: 2.5 per 100K
  
• 6 cases in Wellington-Dufferin-Guelph: 2.2 per 100K
  

Geez those are concerning numbers for WR. Are the Delta variant numbers not being reported?

[ac3r]

One reason our numbers are high is due to outbreaks. There are 29 due to a "congregate setting across multiple locations", whatever that means. I wish they'd be transparent about things. We're in a public health crisis and yet they withhold vital information to the public...

[jeffster]

I did hear through the grapevine that RoW might be the only area not going to Stage 2 if our numbers don't improve. Not sure how valid that grapevine information is though.

The entire province is moving in lockstep. They determined that the different rules in different regions created more problems than they solved.

Unsure of that, Tom. Porcupine isn't moving into stage 1 on Friday, that despite most of the cases being concentrated in the James Bay coastal regions, and not Timmins, for example. Precedent has already been set with them. Stage 2, expect Porcupine, if they're not better, and RoW and possibly Hamilton remaining behind.

[jeffster]

Geez those are concerning numbers for WR. Are the Delta variant numbers not being reported?

RoW and Peel are Delta hotspots right now. Unsure why we're not getting actual numbers though.

Expect boosters to become the norm after 2nd shots, and perhaps of a different kind.

[plam]

Geez those are concerning numbers for WR. Are the Delta variant numbers not being reported?

RoW and Peel are Delta hotspots right now. Unsure why we're not getting actual numbers though.

Expect boosters to become the norm after 2nd shots, and perhaps of a different kind.

Technical issues. There's no simple way to diagnose Delta.

I don't really see evidence yet that boosters will be necessary, though it could happen. Existing vaccines (2 doses) are as effective as we can expect on existing variants.

[ZEBuilder]

Geez those are concerning numbers for WR. Are the Delta variant numbers not being reported?

RoW and Peel are Delta hotspots right now. Unsure why we're not getting actual numbers though.

On the regional website where they report all the covid information they have a section related to variants and mutations. So the region reports the variants including the delta variant of which we have 14 cases of but the provincal government isn't reporting delta cases for whatever reason and Tom is getting his data for variants from the provincal data which is why there is no delta cases on his daily report.

[danbrotherston]

RoW and Peel are Delta hotspots right now. Unsure why we're not getting actual numbers though.

Expect boosters to become the norm after 2nd shots, and perhaps of a different kind.

Technical issues. There's no simple way to diagnose Delta.

I don't really see evidence yet that boosters will be necessary, though it could happen. Existing vaccines (2 doses) are as effective as we can expect on existing variants.

Presumably Delta could be tested for using the same PCR methods that all the other variants are selected for.

And presumably there *are* some numbers for it given that the government is making decisions based on us being a "Delta hotspot"...I'm just wondering why we aren't seeing the numbers.

As for boosters...I think that's a misleading term. The term booster, I've usually seen applied to getting revaccinated for diseases 5-10-20 years later, because our immune memory is not infinite. I don't know that we have a specific term for the seasonal flu vaccine we get, which is essentially a new vaccine every year as it protects against a different strain or variant of the flu.

I don't know if we'll need that, I'm not sure anyone does. The beginning of the pandemic, we seemed to see very little change in the virus, but now we seem to be seeing a lot more variants. I'm not sure why, I would have thought variants would be driven mostly by spread, but I didn't think spread was significantly higher now than in the first year of the pandemic. Perhaps our data is better and we are seeing variants more clearly but I don't think so.

In any case, I don't know how different the variants are from each other, especially in terms of their ability to evade our immune defenses (vaccination driven or otherwise), and how that compares with the flu.

[tomh009]

RoW and Peel are Delta hotspots right now. Unsure why we're not getting actual numbers though.

On the regional website where they report all the covid information they have a section related to variants and mutations. So the region reports the variants including the delta variant of which we have 14 cases of but the provincal government isn't reporting delta cases for whatever reason and Tom is getting his data for variants from the provincal data which is why there is no delta cases on his daily report.

All the quantitative variant reporting is pretty useless. The Alpha/Beta/Gamma processing is slow, and half the results are from who-knows-how-long ago, so about all we can tell is that Alpha is still the most common, and there are a lot of those.

As I recall, testing for Delta requires a full RNA analysis so it is substantially slower yet. Don't know why the province doesn't publish those at all.

Overall, we know Delta is impacting the case rates, but at least from my point of view it's not critical to know the percentage of Delta cases. The total cases (and hospitalization etc) tell the tale anyway, either we are getting this thing under control or not, regardless of the current set of variants.

[tomh009]

I don't know if we'll need that, I'm not sure anyone does. The beginning of the pandemic, we seemed to see very little change in the virus, but now we seem to be seeing a lot more variants. I'm not sure why, I would have thought variants would be driven mostly by spread, but I didn't think spread was significantly higher now than in the first year of the pandemic. Perhaps our data is better and we are seeing variants more clearly but I don't think so.

In any case, I don't know how different the variants are from each other, especially in terms of their ability to evade our immune defenses (vaccination driven or otherwise), and how that compares with the flu.

Essentially, the virus RNA mutates constantly, just like the human DNA does (well, the generational cycle for the viruses is just wee bit faster, but the concept is the same). Most of the mutations end up being either meaningless or actually harmful to the virus, making it unviable. But some combination of mutations have staying power and end up being more "energetic" and viable than their predecessors. And these end up being identified as the variants. (There have been many more variants than these four but they have ended up not spreading as far.)

Challenging conditions (in human bodies, in environment, competing viruses etc) will often result in different mutations succeeding rather than the original. Even the vaccines can cause the virus to mutate to survive. A mere spread will generate more mutations (because there are billions of more viruses that may mutate) and variants, but a spread with difficult conditions will do so at an accelerated pace.

All the variants (to date!) still use the same infection mechanism, and that's why the vaccines still work, even if slightly less effectively. The likelihood is that the variants will evolve further, to the point where a revised vaccine will be needed in order to improve the efficacy. Hopefully not in the next six months, though, so that we can get our initial vaccinations completed, here and worldwide.

[danbrotherston]

I don't know if we'll need that, I'm not sure anyone does. The beginning of the pandemic, we seemed to see very little change in the virus, but now we seem to be seeing a lot more variants. I'm not sure why, I would have thought variants would be driven mostly by spread, but I didn't think spread was significantly higher now than in the first year of the pandemic. Perhaps our data is better and we are seeing variants more clearly but I don't think so.

In any case, I don't know how different the variants are from each other, especially in terms of their ability to evade our immune defenses (vaccination driven or otherwise), and how that compares with the flu.

Essentially, the virus RNA mutates constantly, just like the human DNA does (well, the generational cycle for the viruses is just wee bit faster, but the concept is the same). Most of the mutations end up being either meaningless or actually harmful to the virus, making it unviable. But some combination of mutations have staying power and end up being more "energetic" and viable than their predecessors. And these end up being identified as the variants. (There have been many more variants than these four but they have ended up not spreading as far.)

Challenging conditions (in human bodies, in environment, competing viruses etc) will often result in different mutations succeeding rather than the original. Even the vaccines can cause the virus to mutate to survive. A mere spread will generate more mutations (because there are billions of more viruses that may mutate) and variants, but a spread with difficult conditions will do so at an accelerated pace.

All the variants (to date!) still use the same infection mechanism, and that's why the vaccines still work, even if slightly less effectively. The likelihood is that the variants will evolve further, to the point where a revised vaccine will be needed in order to improve the efficacy. Hopefully not in the next six months, though, so that we can get our initial vaccinations completed, here and worldwide.

I mean, I understand the essential mechanism of evolution here. But I'm not really seeing what conditions changed between early last year, and late last year, early this year to cause more variants. I wouldn't think the vaccine was widespread enough in that timeframe, and the level of spread and containment policies have been more or less the same.

What I meant about how this compares with the flu is that each year the flu virus has mutated somewhat from previous years (and different strains are more or less prevalent), which is why we have new vaccines every year. But we also know that the previous flu vaccines are somewhat effective for new flu variants each year that the old vaccines were not specifically designed for--which is exactly what we are seeing with COVID. What I don't know is how effective the previous flu vaccine is with new variants. For COVID we actually have some numbers on this. But if we had this number for flu vaccines (and I feel like it must be known, or at least knowable), we could start to get an understanding of how likely we are to need a new vaccine every year based on what policies we already use for flu vaccines.

[taylortbb]

Presumably Delta could be tested for using the same PCR methods that all the other variants are selected for.

And presumably there *are* some numbers for it given that the government is making decisions based on us being a "Delta hotspot"...I'm just wondering why we aren't seeing the numbers.

The PCR tests use fluorescing reagents that are keyed to specific genetic sequences. Assuming they're using PCR testing for the mutations, the actual test output is just a yes/no on the N501Y mutation. Currently there's a small enough number of variants that a few specific yes/nos uniquely identify it, but only a full genetic sequencing can really tell what variant a given sample is from.

The delta variant is new enough we don't have tests available that are specifically keyed to its mutations, we can only identify it through genetic sequencing. Obviously however that takes time, and we don't have the capacity to do it to every sample.

What we can do though is read between the lines. My understanding is the Delta variant shows up ambiguously with other variants with the current mutation tests. Specifically, I think it shows up as the "Covid classic" variant, due to not having N501Y or E484K. Therefore if we see a sudden spike in original Covid, as if it suddenly started out competing B117, we can infer it's probably Delta. I believe that's what the province is going on for hot spots.