The COVID-19 pandemic

[tomh009]

THURSDAY 2021-03-04

Waterloo Region reported 33 new cases for today (7.9% of the active cases) and one less for yesterday for a total of 39; 328 new cases for the week (-36), averaging 11.4% of active cases. 402 active cases, +35 in the last seven days.

Next testing report on Friday.

Ontario reported 994 new cases today with a seven-day average of 1,064 (-25). 1,072 recoveries and 10 deaths translated to a drop of 88 active cases and a new total of 10,309. +238 active cases for the week and 108 deaths (15 per day). 65,643 tests for a positivity rate of 1.51%. The positivity rate is averaging 2.22% for the past seven days, compared to 2.42% for the preceding seven.

In the past week there have been 195 cases (+38) of B.1.1.7 (UK), 20 cases (+2) of B.1.351 (SA) and two cases (+0) of P.1 (BR) variant.

281 patients in ICU (+7 today, -2 for the week) and a total hospital population of 649 (-38 for the last seven days).

• 39 cases in Lambton: 29.8 per 100K
  
• 24 cases in Thunder Bay: 16.0 per 100K
  
• 171 cases in Peel: 12.4 per 100K
  
• 9 cases in Northwestern: 10.3 per 100K
  
• 298 cases in Toronto: 10.2 per 100K
  
• 37 cases in Niagara: 8.3 per 100K
  
• 39 cases in Simcoe-Muskoka: 7.2 per 100K
  
• 7 cases in Huron Perth: 7.1 per 100K
  
• 40 cases in Hamilton: 6.9 per 100K
  
• 9 cases in Brant: 6.6 per 100K
  
• 18 cases in Wellington-Dufferin-Guelph: 6.6 per 100K
  
• 33 cases in Halton: 6.0 per 100K
  
• 10 cases in Leeds, Grenville & Lanark: 5.9 per 100K
  
• 64 cases in York: 5.8 per 100K
  
• 49 cases in Ottawa: 4.9 per 100K
  
• 9 cases in Eastern Ontario: 4.4 per 100K
  
• 16 cases in Windsor-Essex: 4.1 per 100K
  
• 23 cases in Waterloo: 3.7 per 100K (based on provincial reporting)
  
• 23 cases in Durham: 3.6 per 100K
  
• 7 cases in Kingston Frontenac: 3.4 per 100K
  
• 6 cases in Southwestern Ontario: 3.0 per 100K
  
• 12 cases in Middlesex-London: 3.0 per 100K
  

Only regions with at least two cases per 100,000 population

[ac3r]

Health Canada approves Johnson and Johnson SARS-CoV-2 vaccine for use in Canada: https://www.cbc.ca/news/politics/johnson...-1.5937900

[ac3r]

Statistics Canada has released some detailed data on how the virus is spreading throughout the country. The vast majority of cases are due to community spread amongst young adults. https://www150.statcan.gc.ca/t1/tbl1/en/...5B2%5D=3.1

[tomh009]

FRIDAY 2021-03-05

Waterloo Region reported 31 new cases for today (7.6% of the active cases) and one less for yesterday for a total of 32; 278 new cases for the week (-50), averaging 9.3% of active cases. 384 active cases, -42 in the last seven days.

An average of 1,847 tests per day in the past week for a positivity rate of 2.15%.

Ontario reported 1,250 new cases today with a seven-day average of 1,063 (-1). 1,159 recoveries and 22 deaths translated to an increase of 69 active cases and a new total of 10,378. +84 active cases for the week and 102 deaths (15 per day). 64,748 tests for a positivity rate of 1.93%. The positivity rate is averaging 2.21% for the past seven days, compared to 2.45% for the preceding seven.

In the past week there have been 322 cases (+127) of B.1.1.7 (UK), 17 cases (-3) of B.1.351 (SA) and two cases (+0) of P.1 (BR) variant. The UK variant increase is a bit of a yellow flag but it's not clear what percentage of tests are being analyzed.

281 patients in ICU (+7 today, -2 for the week) and a total hospital population of 649 (-38 for the last seven days).

• 71 cases in Thunder Bay: 47.4 per 100K
  
• 23 cases in Lambton: 17.6 per 100K
  
• 74 cases in Hamilton: 12.8 per 100K
  
• 167 cases in Peel: 12.1 per 100K
  
• 129 cases in York: 11.6 per 100K
  
• 337 cases in Toronto: 11.5 per 100K
  
• 8 cases in Northwestern: 9.1 per 100K
  
• 47 cases in Halton: 8.6 per 100K
  
• 55 cases in Durham: 8.5 per 100K
  
• 21 cases in Wellington-Dufferin-Guelph: 7.7 per 100K
  
• 47 cases in Waterloo: 7.6 per 100K (based on provincial reporting)
  
• 9 cases in Brant: 6.6 per 100K
  
• 35 cases in Simcoe-Muskoka: 6.5 per 100K
  
• 26 cases in Middlesex-London: 6.4 per 100K
  
• 63 cases in Ottawa: 6.3 per 100K
  
• 23 cases in Windsor-Essex: 5.9 per 100K
  
• 26 cases in Niagara: 5.8 per 100K
  
• 11 cases in Eastern Ontario: 5.4 per 100K
  
• 9 cases in Southwestern Ontario: 4.5 per 100K
  
• 7 cases in Leeds, Grenville & Lanark: 4.1 per 100K
  

Only regions with at least two cases per 100,000 population

[tomh009]

10-day averages for key regions in Ontario, plus the weekly trend as of 2021-03-06 (posting this every two days).

Region	Cases today	per 100K	10-day average	per 100K	Weekly trend
Thunder Bay	54	36.0	43	28.8	+12%
Peel	173	12.5	196	14.2	-13%
Brant	8	5.9	16	12.1	-24%
Lambton	27	20.6	15	11.6	+105%
Toronto	284	9.7	308	10.5	-15%
York	82	7.4	93	8.3	-6%
Hamilton	24	4.1	45	7.8	+2%
Waterloo	33	5.3	46	7.5	-22%
Windsor-Essex	27	6.9	27	7.1	-39%
Wellington-Dufferin-Guelph	17	6.3	18	6.7	+10%
Simcoe-Muskoka	27	5.0	35	6.5	-29%
Northwestern	4	4.6	6	6.3	+59%
Halton	34	6.2	34	6.2	+11%
Durham	32	5.0	35	5.4	+8%
Ottawa	60	6.0	53	5.3	+31%
Eastern Ontario	12	5.9	9	4.6	+26%
Southwestern Ontario	5	2.5	9	4.5	-17%
Niagara	8	1.8	19	4.2	+21%
Huron Perth	7	7.1	4	3.7	+54%
Middlesex-London	8	2.0	13	3.3	+38%
Leeds, Grenville & Lanark	19	11.2	5	3.0	+272%
Ontario total					-11%

[tomh009]

SATURDAY 2021-03-06

Waterloo Region reported 46 new cases for today (11.7% of the active cases) and two more for yesterday for a total of 33; 292 new cases for the week (+14), averaging 9.8% of active cases. 394 active cases, -35 in the last seven days.

Next testing report on Tuesday.

Ontario reported 990 new cases today with a seven-day average of 1,035 (-28). 1,152 recoveries and six deaths translated to a drop of 168 active cases and a new total of 10,210. -269 active cases for the week and 92 deaths (13 per day). 57,829 tests for a positivity rate of 1.71%. The positivity rate is averaging 2.17% for the past seven days, compared to 2.43% for the preceding seven.

In the past week there have been 318 cases (-4) of B.1.1.7 (UK), six cases (-11) of B.1.351 (SA) and six cases (+4) of P.1 (BR) variant.

278 patients in ICU (-2 today, +2 for the week) and a total hospital population of 620 (-60 for the last seven days).

• 54 cases in Thunder Bay: 36.0 per 100K
  
• 27 cases in Lambton: 20.6 per 100K
  
• 173 cases in Peel: 12.5 per 100K
  
• 19 cases in Leeds, Grenville & Lanark: 11.2 per 100K
  
• 284 cases in Toronto: 9.7 per 100K
  
• 82 cases in York: 7.4 per 100K
  
• 7 cases in Huron Perth: 7.1 per 100K
  
• 27 cases in Windsor-Essex: 6.9 per 100K
  
• 17 cases in Wellington-Dufferin-Guelph: 6.3 per 100K
  
• 34 cases in Halton: 6.2 per 100K
  
• 60 cases in Ottawa: 6.0 per 100K
  
• 12 cases in Eastern Ontario: 5.9 per 100K
  
• 8 cases in Brant: 5.9 per 100K
  
• 33 cases in Waterloo: 5.3 per 100K (based on provincial reporting)
  
• 27 cases in Simcoe-Muskoka: 5.0 per 100K
  
• 32 cases in Durham: 5.0 per 100K
  
• 4 cases in Northwestern: 4.6 per 100K
  
• 24 cases in Hamilton: 4.1 per 100K
  
• 5 cases in Southwestern Ontario: 2.5 per 100K
  

Only regions with at least two cases per 100,000 population

[tomh009]

SUNDAY 2021-03-07

Waterloo Region reported 39 new cases for today (9.7% of the active cases) and eight more for yesterday for a total of 54; 291 new cases for the week (-1), averaging 9.9% of active cases. 383 active cases, -57 in the last seven days.

Next testing report on Tuesday.

Ontario reported 1,299 new cases today with a seven-day average of 1,069 (+34). 1,105 recoveries and 15 deaths translated to an increase of 179 active cases and a new total of 10,389. -103 active cases for the week and 87 deaths (12 per day). 46,586 tests for a positivity rate of 2.79%. The positivity rate is averaging 2.26% for the past seven days, compared to 2.41% for the preceding seven.

In the past week there have been 300 cases (-18) of B.1.1.7 (UK), four cases (-2) of B.1.351 (SA) and 10 cases (+4) of P.1 (BR) variant.

273 patients in ICU (-5 today, -16 for the week).

• 53 cases in Thunder Bay: 35.3 per 100K
  
• 21 cases in Lambton: 16.0 per 100K
  
• 89 cases in Hamilton: 15.4 per 100K
  
• 38 cases in Wellington-Dufferin-Guelph: 14.0 per 100K
  
• 192 cases in Peel: 13.9 per 100K
  
• 329 cases in Toronto: 11.2 per 100K
  
• 116 cases in York: 10.5 per 100K
  
• 59 cases in Waterloo: 9.5 per 100K (based on provincial reporting)
  
• 58 cases in Durham: 9.0 per 100K
  
• 12 cases in Brant: 8.8 per 100K
  
• 32 cases in Windsor-Essex: 8.2 per 100K
  
• 33 cases in Niagara: 7.4 per 100K
  
• 29 cases in Middlesex-London: 7.2 per 100K
  
• 7 cases in Huron Perth: 7.1 per 100K
  
• 39 cases in Halton: 7.1 per 100K
  
• 36 cases in Simcoe-Muskoka: 6.7 per 100K
  
• 5 cases in Northwestern: 5.7 per 100K
  
• 48 cases in Ottawa: 4.8 per 100K
  
• 5 cases in Chatham-Kent: 4.7 per 100K
  
• 8 cases in Leeds, Grenville & Lanark: 4.7 per 100K
  
• 9 cases in Eastern Ontario: 4.4 per 100K
  

Only regions with at least two cases per 100,000 population

[tomh009]

10-day averages for key regions in Ontario, plus the weekly trend as of 2021-03-08 (posting this every two days).

Region	Cases today	per 100K	10-day average	per 100K	Weekly trend
Thunder Bay	91	60.7	49	32.9	+67%
Lambton	19	14.5	19	14.8	+39%
Peel	322	23.3	202	14.6	+14%
Brant	20	14.7	18	12.9	-69%
Toronto	568	19.4	319	10.9	+46%
York	119	10.7	95	8.6	+21%
Hamilton	22	3.8	48	8.2	-2%
Northwestern	11	12.5	7	8.1	-3%
Waterloo	51	8.3	46	7.4	-6%
Wellington-Dufferin-Guelph	10	3.7	20	7.3	-4%
Halton	51	9.3	37	6.8	+18%
Windsor-Essex	46	11.8	26	6.7	+47%
Durham	68	10.5	40	6.3	+76%
Simcoe-Muskoka	48	8.9	33	6.2	+26%
Ottawa	57	5.7	57	5.7	-3%
Niagara	31	6.9	22	5.0	+54%
Sudbury	27	6.9	19	4.9	+100%
Eastern Ontario	15	7.4	10	4.7	+72%
Huron Perth	4	4.1	4	4.5	+25%
Southwestern Ontario	4	2.0	9	4.4	-95%
Middlesex-London	18	4.4	17	4.2	+43%
Leeds, Grenville & Lanark		.0	6	3.7	+115%
Chatham-Kent	5	4.7	2	2.2	+133%
Ontario total					+26%

[tomh009]

In the past week there have been 300 cases (-18) of B.1.1.7 (UK), four cases (-2) of B.1.351 (SA) and 10 cases (+4) of P.1 (BR) variant.

So, it turns out that this really is quite misleading. Not all samples can be tested for the N501Y mutation (which all of the above variants have); the number screened for N501Y seems to fluctuate around 1,000 per day, or only about 2% of the total number of COVID-19 tests.

The percentage of these that test positive for N501Y has gone up from about 15% in mid-February to over 30% recently.

These samples then go through genome sequencing to determine whether they match one of the above variants; this takes multiple days. It's not clear whether all N501Y-positive are sequenced. If they do sequence all of them, then it appears that the variant positivity rate is somewhere below 20%.

But applying the 30% N501Y positivity rate and the 20% variant positivity rate means that maybe somewhere between 5% and 15% of the COVID samples (that are tested for N501Y) are positive for one of the variants. The case numbers posted make it look like the variants make up only about 0.1% of the cases in Ontario, but I think, based on the data above, that the actual percentage of variants may be between 10x and 100x that.

I'm going to stop posting the variant numbers until I can determine some more meaningful numbers.

[ZEBuilder]

So, it turns out that this really is quite misleading. Not all samples can be tested for the N501Y mutation (which all of the above variants have); the number screened for N501Y seems to fluctuate around 1,000 per day, or only about 2% of the total number of COVID-19 tests.

...

But applying the 30% N501Y positivity rate and the 20% variant positivity rate means that maybe somewhere between 5% and 15% of the COVID samples (that are tested for N501Y) are positive for one of the variants. The case numbers posted make it look like the variants make up only about 0.1% of the cases in Ontario, but I think, based on the data above, that the actual percentage of variants may be between 10x and 100x that.

From a quick look at the Waterloo region covid dashboard it has the UK variant and then screened positive for a variant on the dashboard and the screened positive is more than 10x the amount of the UK. So it seems that the province is just reporting on cases where the lineage is determined so the actual number of cases of variants is 10x the value reported based upon what the region reports.

That also means that since theres only 2% of the total tests screened for N501Y the value of total variants in total should be 50x's larger then what's reported. Ontop of that there's 10x's more than what's reported in that 2% based upon the above which means we could be looking at 500x's more variant cases than what's reported.

[plam]

In the past week there have been 300 cases (-18) of B.1.1.7 (UK), four cases (-2) of B.1.351 (SA) and 10 cases (+4) of P.1 (BR) variant.

So, it turns out that this really is quite misleading. Not all samples can be tested for the N501Y mutation (which all of the above variants have); the number screened for N501Y seems to fluctuate around 1,000 per day, or only about 2% of the total number of COVID-19 tests.

The percentage of these that test positive for N501Y has gone up from about 15% in mid-February to over 30% recently.

These samples then go through genome sequencing to determine whether they match one of the above variants; this takes multiple days. It's not clear whether all N501Y-positive are sequenced. If they do sequence all of them, then it appears that the variant positivity rate is somewhere below 20%.

But applying the 30% N501Y positivity rate and the 20% variant positivity rate means that maybe somewhere between 5% and 15% of the COVID samples (that are tested for N501Y) are positive for one of the variants. The case numbers posted make it look like the variants make up only about 0.1% of the cases in Ontario, but I think, based on the data above, that the actual percentage of variants may be between 10x and 100x that.

I'm going to stop posting the variant numbers until I can determine some more meaningful numbers.

Probably 30% (and 40% in Toronto) are about right. Someone suggested to me that 2% may be the positive tests which are all sent for sequencing.

[tomh009]

MONDAY 2021-03-08

Waterloo Region reported 51 new cases for today (13.2% of the active cases) and no more for yesterday for a total of 39; 307 new cases for the week (+16), averaging 10.6% of active cases. 390 active cases, -43 in the last seven days.

Next testing report on Tuesday.

Ontario reported 1,631 new cases today -- although a few hundred of those were apparently prior cases reported now due to some data lag -- with a seven-day average of 1,155 (+86). 994 recoveries and 10 deaths translated to an increase of 627 active cases and a new total of 11,016. +449 active cases for the week and 88 deaths (13 per day). 38,063 tests for a positivity rate of 4.29%. The positivity rate is averaging 2.46% for the past seven days, compared to 2.48% for the preceding seven.

282 patients in ICU (+9 today, +2 for the week).

• 91 cases in Thunder Bay: 60.7 per 100K
  
• 322 cases in Peel: 23.3 per 100K
  
• 568 cases in Toronto: 19.4 per 100K
  
• 20 cases in Brant: 14.7 per 100K
  
• 19 cases in Lambton: 14.5 per 100K
  
• 11 cases in Northwestern: 12.5 per 100K
  
• 46 cases in Windsor-Essex: 11.8 per 100K
  
• 119 cases in York: 10.7 per 100K
  
• 68 cases in Durham: 10.5 per 100K
  
• 51 cases in Halton: 9.3 per 100K
  
• 48 cases in Simcoe-Muskoka: 8.9 per 100K
  
• 51 cases in Waterloo: 8.3 per 100K (based on provincial reporting)
  
• 15 cases in Eastern Ontario: 7.4 per 100K
  
• 27 cases in Sudbury: 6.9 per 100K
  
• 31 cases in Niagara: 6.9 per 100K
  
• 57 cases in Ottawa: 5.7 per 100K
  
• 5 cases in Chatham-Kent: 4.7 per 100K
  
• 18 cases in Middlesex-London: 4.4 per 100K
  
• 4 cases in Huron Perth: 4.1 per 100K
  
• 22 cases in Hamilton: 3.8 per 100K
  
• 10 cases in Wellington-Dufferin-Guelph: 3.7 per 100K
  

Only regions with at least two cases per 100,000 population

[tomh009]

TUESDAY 2021-03-09

Waterloo Region reported 27 new cases for today (6.9% of the active cases) and four more for yesterday for a total of 55; 289 new cases for the week (-18), averaging 10.1% of active cases. 358 active cases, -87 in the last seven days.

An average of 2,233 tests per day for the last week for a positivity rate of 1.85%.

Ontario reported 1,185 new cases today with a seven-day average of 1,187 (+32). 972 recoveries and six deaths translated to an increase of 207 active cases and a new total of 11,223. +667 active cases for the week and 86 deaths (12 per day). 33,264 tests for a positivity rate of 3.56%. The positivity rate is averaging 2.52% for the past seven days, compared to 2.26% for the preceding seven.

290 patients in ICU (+8 today, +6 for the week) and a total of 689 hospital beds in use (+12 for the week).

N509Y mutation testing was 30.3% positive, averaging 32.2% for the past week.

• 39 cases in Thunder Bay: 26.0 per 100K
  
• 235 cases in Peel: 17.0 per 100K
  
• 81 cases in Hamilton: 14.0 per 100K
  
• 343 cases in Toronto: 11.7 per 100K
  
• 14 cases in Lambton: 10.7 per 100K
  
• 11 cases in Chatham-Kent: 10.4 per 100K
  
• 9 cases in Northwestern: 10.3 per 100K
  
• 105 cases in York: 9.5 per 100K
  
• 48 cases in Halton: 8.8 per 100K
  
• 30 cases in Windsor-Essex: 7.7 per 100K
  
• 46 cases in Waterloo: 7.4 per 100K (based on provincial reporting)
  
• 24 cases in Sudbury: 6.2 per 100K
  
• 30 cases in Simcoe-Muskoka: 5.6 per 100K
  
• 21 cases in Middlesex-London: 5.2 per 100K
  
• 10 cases in Eastern Ontario: 4.9 per 100K
  
• 22 cases in Niagara: 4.9 per 100K
  
• 45 cases in Ottawa: 4.5 per 100K
  
• 6 cases in Brant: 4.4 per 100K
  
• 7 cases in Leeds, Grenville & Lanark: 4.1 per 100K
  
• 25 cases in Durham: 3.9 per 100K
  
• 10 cases in Wellington-Dufferin-Guelph: 3.7 per 100K
  
• 5 cases in Southwestern Ontario: 2.5 per 100K
  
• 2 cases in Huron Perth: 2.0 per 100K
  
• 1 cases in Kingston Frontenac: 0.5 per 100K
  

Only regions with at least two cases per 100,000 population

[ac3r]

11 local cases now linked to a couple of dumbasses throwing a wedding on Monday: https://outline.com/UDwywG

May their marriage end in swift, expensive divorce.

[tomh009]

N509Y mutation testing was 30.3% positive, averaging 32.2% for the past week.

... and this data now not included in the daily epidemiologic summaries. Sigh. I think these charts show us where things are going though: