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February 5, 2021 - Dr. Archer's Update on COVID-19 response from the DOM and Medicine Program


All patients admitted to KHSC will undergo Covid-19 testing

1) All about COVID-19 Vaccines: 

  • Perspective-the rush to vaccinate prior to spread of variant virus and the need to take a global approach to vaccination (how equity serves safety).
  • Update on global vaccination programs (click here
  • Results from Canada’s vaccine safety monitoring system provides reassurance of safety (click here), 
  • Updated FAQs about vaccination effectiveness against viral variants and safety of vaccination for people on blood thinners, with allergies or people who are immunosuppressed 
  • Updates on Canada’s vaccination program (click here)

2) KHSC has received no new COVID-19 patients from Toronto since initial transfers (but we remain on standby) 

3) Ontario’s epidemic is much better controlled since the lockdown with lower rates of new cases (1563 new case yesterday) and a fall in rate of test positivity to 2.2% (click here).

4) KFL&A COVID-19 rates remain amongst the lowest in the province (see update from KFL& A Public Health)

5) Canada’s COVID-19 epidemic continues to improve: There have been 792,440 total cases to date and 89.7% are resolved. For the first time in wave two there is a decrease in new cases, active cases, hospitalizations and deaths (click here) (click here). 

6) The COVID-19 global pandemic: Active case rates is declining (click here) and positive test rates in the USA decline to levels last seen in July 2020:


1) All about COVID-19 Vaccines: 

  • Perspective-the rush to vaccinate prior to spread of variant virus and the need to take a global approach to vaccination (how equity serves safety).
  • Update on global vaccination programs (click here
  • Results from Canada’s vaccine safety monitoring system provides reassurance of safety (click here), 
  • Updated FAQs about vaccination effectiveness against viral variants and safety of vaccination for people on blood thinners, with allergies or people who are immunosuppressed 
  • Updates on Canada’s vaccination program (click here)

Perspective on why we need to act globally: Rich countries have vaccines; poor countries do not. In Canada we are understandably frustrated in by the slow vaccine rollout; but we can be fairly confident that we will be vaccinated sometime this year. People in low income countries are not so fortunate. This is unacceptable for several reasons, one related to social justice and the other to the nature of viral infections.

Let’s begin at home. Canada is appropriately under pressure to vaccinate its residents not just to save lives and allow reopening of society. There is also time sensitivity, because the longer the with the majority of people still susceptible to the virus the more damage the new highly infectious viral variants (mutants) can do. The risk to a large number of vulnerable Canadians of the rapidly evolving and mutating SARS-CoV-2 is real.Just in the last week or two there is yet a new mutation of the already mutated “British variant” of the virus. This new mutation is called E484K, and this mutation is also found in the highly contagious Brazilian and South African variants (click here). The mutation makes it easier for the virus to bind to human cells and evade antibodies. These mutations don’t defeat the vaccine but it does reduce vaccine effectives a bit.

The South African variant has three or more mutations and is more resistant to existing vaccines than the original SARS-CoV-2. Early reports related to the newer vaccines from Novavax and Johnson & Johnson, reportedly show less effectiveness against these mutant viruses. Novavax says its vaccine is 89.3% effective overall in the UK. Their study included 50% of people infected with the UK variant virus (click here). Whilst the vaccine was 95.6% effective against the original COVID-19 strain it was only 85.6% effective against the UK variant strain. This vaccine is also effective against the South African variant, however once again less so than against the original coronavirus, offering only 60% protection in a population where most infections were caused by the South African mutation variant (unpublished data (click here).

Screenshot of Novavax press release with company logo

Also in unpublished data, Johnson & Johnson said the level of protection of its new vaccine is 72% in the United States, 66% in Latin America and 57% in South Africa (click here). These effectiveness numbers sound low but it there is some good news from the Phase 3 ENSEMBLE trial (conducted in eight countries across three continents including 34% (N= 14,672) of participants over age 60). The study shows that the J&J vaccine offers complete protection against hospitalization and deaths, 28 days post-vaccination (click here). So, while there may still be risk of infection the vaccine it eliminates the really bad infections!

screenshot of Johnson and Johnson vaccine efficacy news article with Johnson and Johnson logo

The longer we leave populations unvaccinated the more chance the virus has to acquire mutations, many of which will increase its infectivity or lethality. The virus doesn’t care if these unvaccinated people are rich or poor! If we could mass vaccinate globally viral spread would stop and with it mutation generation. This would quickly end the pandemic.

But will rich countries share vaccine? In a recent Nature paper, Canada doesn’t look great in this regard. We have more secured vaccine per person than any other country (click here).

Ranking of countries who are best supplied to worst supplied with vaccine

Canada has done well to secure vaccines-it will do well to share them!

The article notes, “Low- and middle-income countries are let to rely on on contributions from COVAX, a joint fund for equitable distribution of COVID-19 vaccines led by Gavi, a funder of vaccines for low-income countries based in Geneva, Switzerland, the World Health Organization, and the Coalition for Epidemic Preparedness Innovations (CEPI) in Oslo” (click here). They have secured 700 million vaccine doses so far and want to provide 2 billion by the end of 2021. They have the goal of supplying 20% of the population of participating countries. More than 189 countries have signed up to COVAX, including wealthy economies that have joined to subsidize vaccine access.” 

However, even if they reach this goal (which depends on wealthy countries) this leaves many people unvaccinated.In addition to compassion for our fellow humans, this represents a problem. As long as large groups of people (billions) are unvaccinated the virus can thrive and mutate. Ultimately our own greed/apathy would come back to bite us as these future mutants might well evade vaccines and reinfect people in rich countries. 

So, we need to do right by all people. Canada has recently drawn criticism by being the first country to use some of the vaccine it had offered to COVAX for our own domestic use (done because our domestic supply chain was disrupted) (click here). Once we get our momentum in domestic vaccination we need to share our (anticipated) vaccine wealth; not for charity, nor for praise, but because it is both ethical and a part of the solution to end the pandemic.

Global vaccine progress: Here is a snapshot on how we are doing globally in administering vaccine (presented as # of vaccines administered/100 people/country). Israel is doing the best and Canada is well down the pack at #19)(click here). No vaccine came to Canada last week which did not help the cause!

two graphs side by side showing Global Vaccine progress line graph on left with lots of coloured lines and bar graph on right

Global vaccine progress, Feb 4th 2021

Vaccination roll-out update (click here): We are on a roll-but it’s a slow roll. There has been VERY little progress since Monday, the result of a limited supply chain from Pfizer. Ironically we now have the means to rapidly vaccinate people-we just need vaccine from Pfizer and Moderna. 

As of today a total, 1,157,940 doses of COVID-19 vaccines (including both Moderna and Pfizer-BioNTech) have been delivered. Thus far, 87.4% of delivered doses have been administered. As of today, 875,277 Canadians have received at least one dose of an approved COVID-19 vaccine (see below-number revised down from Monday-not sure why). At least 1136,236 Canadians are fully vaccinated (only 23,000 more than Monday)(click here).

map of Canada with each province labelled and the number of vaccine doses administered to date

Number of vaccinations in arms as of Feb 4th 2021

The priority population for our first vaccines in Ontario are residents and staff of long term care (LTC facilities). A recent CTV report quotes the Ontario government as saying (click here) that ~47,000 residents of Ontario LTC homes have received the first dose of the vaccine with another ~17,000 awaiting the vaccine. Approximately 3,000 residents have refused the first dose.

Based on the clinical trials and experience in millions of people who have been vaccinated world-wide we can be reassured of both their safety and efficacy. All the side effects (called adverse events and abbreviated AEFI) are tracked and reported by the government of Canada. Here is what we have seen to date (no update since Jan 15th) (click here). It is frustrating that the government has not updated their own adverse effect site in 3 weeks.

Here are answers to some updated FAQs with answers to common questions about the COVID-19 vaccines.

FAQ 1) Does the vaccine work against new variants (mutations) in the SARS-CoV2 virus? Short answer is a qualified YES. The vaccines work albeit not quite as well for the variants. This slide below (from Dr Evans) shows results from 144,000 participants in randomized clinical trials (RCTs, including both the vaccinated and the unvaccinated). In those receiving any active vaccine there there are only 3 cases of severe COVID-19 (vs 37 in the control group). There were no deaths in people who were vaccinated with any of the vaccines versus 5 deaths in the control group. As discussed at the beginning of this section, even though absolute protection is slightly less for UK and South African variants the vaccines have a preserved ability to prevent serious adverse outcomes (like hospitalization and death). Thus, despite variant viruses the vaccines are lifesavers!

excel spreadsheet showing the safety of each vaccine by manufacturer

Vaccines are safe and effective: RCT data

FAQ 2) I’m on a blood thinner, can I be vaccinated for COVID-19? Short answer YES. Here is a more detailed answer from an Canadian agency with expertise on the use of blood thinners, Thrombosis Canada

memo for people on blood thinners getting the vaccine

FAQ 3) I have a history of allergic reactions, can I be vaccinated for COVID-19? Short answer YES. Out of ~1.8 million vaccinations there have only been 21 reported episodes of anaphylaxis (the most serious type of allergic reaction). Most (70%) of these events occurred within 15 minutes of the vaccine (while the patient is still being monitored, as summarized in a Jan 6th MMWR CDC article). There were also 83 cases of non-anaphylaxis allergic reaction after Pfizer-BioNTech COVID-19 vaccination with symptom onset within the 0–1-day risk window. Most (87%) of these allergic reactions were classified as non-serious.

logo for Centers for Disease Control and Prevention Morbidity and Mortality weekly report

So while there is not zero risk, the risk of severe allergic reactions to the Pfizer vaccine are low and manageable. Allergy testing is NOT necessary prior to COVID-19 vaccination even in people with history of allergies. It is important note that none of the people who developed anaphylaxis after vaccination died and most did not have a prior history of anaphylaxis (see table below). The incidence of anaphylaxis is lower still with the Moderna vaccine.

The adverse effects of the COVID-19 vaccines clinical trials are similar in vaccinated people vs people (in the clinical trial who got a placebo-saline injection) except for local pain at the vaccine site and increased muscle ache and headache, all of which were short-term (see below). This is a very good safety profile relative to other vaccines.

table listing side effects of Pfizer vaccine vs placebo

The CDC does advise against the use of the two mRNA vaccines for a very select group of people with the following allergy histories (click here):

CDC considers a history of the following to be a contraindication to vaccination with both the Pfizer-BioNTech and Moderna COVID-19 vaccines:

  • Severe allergic reaction (e.g., anaphylaxis) after a previous dose of an mRNA COVID-19 vaccine or any of its components
  • Immediate allergic reaction of any severity to a previous dose of an mRNA COVID-19 vaccine or any of its components (including polyethylene glycol [PEG])*
  • Immediate allergic reaction of any severity to polysorbate (due to potential cross-reactive hypersensitivity with the vaccine ingredient PEG)*

FAQ 4) I’m immunosuppressed, should I get vaccinated? This question has a less clear answer. First, be reassured is no virus (dead or alive) in the Pfizer or Moderna vaccines so it is not possible for a person to get infected from the vaccine. However immunosuppressed people were not included in the initial clinical trials. That said, they probably are safe to be vaccinated but this is more a matter of expert opinion. In Canada the National Advisory Committee on Immunization (NACI) currently advises that the COVID-19 vaccine should not be offered to populations excluded from clinical trials “until further evidence is available.” However, they also say (an immunosuppressed person or those with an autoimmune disorder can still be vaccinated if a risk assessment deems that the benefits of vaccine outweigh the potential risks for the individual.” (click here).

The British Society for Immunology recently issued a statement indicating that vaccination is safe in immunosuppressed people (click here), albeit the resulting immune response may be weaker. They remind us that because there is no virus in the vaccine there is absolutely no risk of acquiring COVID-19 from the vaccine.

Our own Dr. Mike Beyak (gastroenterology) nicely summarized evidence from a registry of ~4500 patients who were immunosuppressed for their inflammatory bowel diseases (Crohn’s disease and ulcerative colitis) at this morning’s Zoom Medical Grand Rounds (see below). There was no increased risk of contracting COVID-19 in these 4500 patients. Apart for patients on prednisone, there was also no increased complications from COVID-19 when it occurred. Interestingly, some biologic therapies (antibody treatments for IBD) actually appear to reduce adverse outcomes in IBD patients who contracted COVID-19. This is not surprising since the truly bad outcomes in COVID-19 seem to occur in people who mount a hyper-aggressive immune response. 

Overall these data are good news for our many patients with rheumatoid arthritis, asthma and IBD who are on immunosuppressive therapies. However, since these people were not included in the vaccine clinical trials, it is advised they consult the physicians/clinic that is managing their care to inform their vaccine decision.

FAQ 5: How long can I wait after my first dose to get a second vaccine dose? The Ontario science table which deals with COVID-19 (on which our own Dr Evans participates) has looked at the efficacy of delaying the second vaccine dose to 42 days. It appears a second dose at day 42 is as effective in producing a neutralizing antibody response as when the dose is given at day 21 (the normal interval from dose 1). This more lenient 42-day protocol has been approved by Health Canada.

needle and syringe drawing vaccine from a bottle

2) KHSC received no new COVID-19 patients from Toronto since the initial 4 ICU transfers over a week ago; but we remain on standby 

We remain on standby to receive patients from Toronto and Scarborough but no cases arrived over the past week since we received 4 ICU patients. 

3) Ontario’s epidemic is much better controlled since the lockdown with lower rates of new cases (1563 new case yesterday) and a fall in rate of test positivity to 2.2% (click here).

The situation is markedly improved in Ontario with new case rates below 2000 (1563 yesterday, see below), low rates of positive tests and declining rates of hospitalization. If it were not for the emergence of mutant virus and the slowness of vaccination delivery we would be out of the woods. However, between these two realities and the existence of local hotspots, continued public health vigilance is still required. Nonetheless these changes are promising for the not too distant reopening of Ontario. Since the pandemic began ~5% of infected people in Ontario have been hospitalized and 2.3% of infected people have died.

box with text and numbers

Rates of new cases and positive tests are half what they were pre lockdown on Dec 26th 2020

We have had a 24% reduction in new cases this week, compared to the prior week. Likewise, hospitalizations have declined 20% (see below).

pink bar graph

A big improvement in rates of hospitalizations and new cases in Ontario

Peel (on Toronto’s western border) remains the hot spot in Ontario with 319.8 recent cases/100,000 population (click here). A look at recent infections (infections within the past 2 weeks, expressed as cases/100,000 population) in other areas shows:

Rate of cases/100,000 population in the past 2 weeks in various areas (all rates are decreasing compared with last week)






photo of toronto waterfront taken from the water with CN tower and Roger's centre in the background

Rates of COVID-19 infection in Toronto vary widely amongst neighbourhoods. The burden of COVID-19 disproportionately affects black, middle eastern and southeast Asian populations (relative to whites). Since the pandemic began, the Thistletown-Beaumond neighbourhood has had 7,645 cases/100,000 residents, ~ 10X the burden of COVID-19 in the Beaches neighbourhood (798 cases of COVID-19/100,000 residents). When one examines recent cases, those since Jan 6th 2021, case prevalence is still high, ranging from 84 cases/100,000 residents in St. Andrews-Windfield to 1030 cases/100,000 residents in Henry Farm (click here).

We should avoid elective travel to and from these hot spots from lower prevalence areas, like Kingston.

4) KFL&A COVID-19 rates remain amongst the lowest in the province (see update from KFL& A Public Health)

The total number of cases in KFL&A since the pandemic began has increased 5 since Monday and is now 672, not counting the prison outbreak. There has only been one death of a KFL&A resident since the pandemic began. There are 13 active cases in the community, up from 11 active cases on Monday. There are 2 COVID-19 patient hospitalized at KGH (down from 5 last week). There are 41 active cases in SE Ontario. 

5) Canada’s COVID-19 epidemic continues to improve: There have been 792,440 total cases to date and 89.7% are resolved. For the first time in wave two there is a decrease in new cases, active cases, hospitalizations and deaths (click here) (click here). 

Our second wave of COVID-19 (orange line-top panel below) has been improving for several weeks, with a continuing 20% decline in the weekly rates of new cases (see below). We are now seeing the expected fall in hospitalizations, 13% down last week compared to the week before (table below). ~89.7 % of all cases have already recovered. There have been 20,487 COVID-19 deaths thus far (a cumulative national case mortality rate of ~1.97%). Canada has performed 22.426 million COVID-19 tests with a cumulative test positivity rate of 3.52%.

pink bar graph

Decline in new and active cases, hospitalizations and deaths this week in Canada (click here).

Rates of infection have plateaued in all Western provinces (BC to Manitoba) as a result of introduction of more aggressive public health measures. Saskatchewan too has now seen a decline in rates and assumed a new lower plateau trajectory. Rates in Ontario and Quebec (home to almost 63% of all Canadians) are experiencing a lockdown-induced decline. Rates of new infection have remained begun to decrease in New Brunswick. Infection rates remain flat in the other Maritime provinces. The outbreaks in the North have been controlled with few new cases in the NWT, Yukon, and Nunavut.

7) The COVID-19 global pandemic: Active case rates is declining (click here) and positive test rates in the USA decline to levels last seen in July 2020:

The global case burden for COVID-19 is 104,694,138 total cases with 2,277,590 deaths, a 2.18% case mortality rate. The UK has seen more than 110,000 COVID-19 deaths. The new variant is now the dominant form of the virus in Britain. While more contagious it is unclear whether the virus is more lethal once contracted. Other variants that have emerged include the B.1.351 variant in South Africa and the P.1 variant in Brazil. 

The number of cases globally has increased >6-fold since early August, 2020, when there were 16 million cases. The pandemic hot spots are in the USA, India, Brazil, the United Kingdom and Russia. A positive note is the decline in the daily number of active cases (see bottom right orange graph).

world map with dots denoting large amounts of covid. ranking of countries by name on the side

Global COVID-19: The number of active cases world-wide (salmon dots on map) is declining (orange graph on right)-Feb 4th 

The USA, with 26,623,742 cases and 454,060 deaths, tops the COVID-19 list and accounts for ~25% of the global pandemic (up from 21% pre-Christmas). The USA only accounts for ~4% of the world’s population (see below). There are as many cases in America as in India, Brazil, UK and Russia combined! The ONLY solutions to this are adherence to public health measures and rapid mass vaccination.

Improving USA positive test rates (click here): The USA has seen continued improvement in positive test rate for several weeks and is now at 7.7%, the lowest since July 2020 (click here) (see below). 

line graph over bar graph

Continued improvement in positive test rates in the USA, Feb 4th 2021

The US-Canadian border closure has been extended until at least Feb 21st, 2021 (click here). That said, Canadians can still fly to America (certain rules apply) and as discussed in my note in early December, Canadian citizens can return to Canada from America, with a number of new requirements, including negative COVID-19 tests and quarantine, discussed earlier in this note, point #2).

land border bridge with Canadian and USA flags in the forefront

Regular reminders

KHSC bed capacityBed capacity is adequate with 61 beds available (down 12 from Monday) and good ventilator capacity (see graphic below). Our ventilator supply remains good; however, critical care beds are in short supply (see below). Medicine remains busy with our doctors caring for people in 181 beds, not including ICU beds on Davies 4 staffed by the Medicine program. 

half circle meter with numbers to the right

We are committed to providing care to the 99.9% of patients in SE Ontario who do not have COVID-19. In addition to acute care for heart attacks, strokes and trauma etc., we are continuing to provide elective care. We recognize that the term “elective care” is really a misnomer. Many “elective” patients have chronic pain and disability or suffer from cancer and other serious diseases and will not tolerate delay in care. We continue to encourage physicians to optimize the use of e-health visits. We are also reminding patients who are coming to clinics in person that unless it is essential (and approved) they need to come alone, to minimize crowding in our clinic waiting areas. That said, it remains VERY safe to attend appointments at our clinics or to come to hospital for needed care!

Use the Mobile Screening Tool to expedite clinic visits: Complete the COVID-19 pre-screening tool hereand you will be able to “skip the line”: One way to safely expedite entry of patients into our facilities is to have all patients complete our pre-screening questionnaire before their clinic visit. This will screen out people who are sick and expedite entry to the facility for everyone. Reducing lines waiting to enter the clinics will be particularly important as colder weather arrives. The mobile screening tool only takes a few minutes to complete and you will receive an email with confirmation to bring with you, along with your appointment slip, in printed form or on your mobile device. To complete the mobile-screening in English, click here and in French, click here.

screenshot of KHSC prescreening app with index finger scrolling on iPhone

KHSC visitor policy: One of the hardest aspects of COVID-19 care in the hospital is the need to restrict visitors to ensure we don’t import COVID-19 into the hospital. If a family member is coming in from a high prevalence area they cannot enter KHSC (i.e. they will fail the screening question). There are exceptions made for exceptional circumstances; but this policy is necessary to prevent importation of infection to the hospital which would impair our ability to care for all patients. A very few cases of COVID-19 can paralyze the hospital, particularly if they are brought in by visitors and then spread undetected. All details on the policy can be found using this link (click here). 

COVID-19 testing at Beechgrove Community Assessment Center: (click here): All COVID-19 test must be scheduled appointments (versus walk in). Appointments can be scheduled using our on line scheduling system. Before booking a test, individuals should complete the online tool to determine whether they qualify for testing (click here). Operating hours: Testing hours will return to 9 a.m. to 4 p.m. daily. To be tested you will require: A valid Ontario health card or a piece of photo identification. You must also wear a mask and maintain physical distancing at all times while in the walk-in line (click here).

animated photo of female getting a covid nasal swab testthree young boys dressed as doctors with their arms folded across their chests and wearing stethoscope

Because health care workers (doctors and staff) are increasingly having to miss work because their children have been sent home from school or daycare with symptoms of a upper respiratory tract infection, we have arranged that their children can access expedited testing at Beechgrove . The goal of this service is simply to allow the healthcare worker to return to work as quickly as possible for the public good. The children of staff will be tested between 1230 -1300 by appointment, 7 days/week. The new program for families applies to children up to age 18, an includes children of staff and physicians who provide clinical care and service. Staff and physicians themselves should contact occupational health to book their testing appointment. To book an appointment for a child, KHSC staff should call 613-548-2376. Testing of clinical staff and faculty and their children is processed at the KHSC lab with an average turnaround time of less than 24 hours.

Increased outbreaks and deaths in Long Term Care facilities (LTC): As discussed in many prior notes, most COVID-19 deaths occur in people who are not only old but who are also frail and live in nursing homes and LTC. As of today, the 3,627 deaths in nursing homes (up 98 deaths since Monday) account for ~57.3% of all deaths in Ontario, click here. There are also ~ 701 active cases in LTC residents and 758 active cases in LTC staff (numbers which are continuing to decrease)! In the last month the rate of death amongst LTC residents has continued to increase daily and is now >100/week! The good news is the number of infections in LTCs in staff and residents is declining rapidly. Outbreaks in nursing homes usually imported by a person coming in from the community (health worker or family) acquiring the infection and importing it into the facility. Thus, protecting LTCs is best done with a combination of reducing community spread of COVID-19 and ensuring single occupancy rooms in LTCs (as well as appropriate pay for PWS workers, provision of PPE and rapid testing capacity). It is because of these grim statistics (see below) that the province has prioritized vaccination of health care workers and residents of Ontario’s LTCs.

three masked people sitting at a table with one older man in a wheelchair

COVID-19 in toddlers and young children: (click here). School is back (in 7 regions) and with this a return to reporting on COVID-19 in schools. The good news is the reopening in the 7 areas where it was permitted has not resulted in major increases in new cases. Below is the new baseline report for school age children in publicly funded Ontario schools. School boards report every weekday from Monday to Friday. There have been 5172 students with COVID-19 since the pandemic began; 14 new cases in the past 2 weeks (see below).

four teenagers sitting on a bench each using an iPhone or iPad and one reading a book

Here are the parallel data from licensed childcare facilities in Ontario-where there have been 1134 children infected since the pandemic began, 174 new cases in the past 2 weeks.

group of young children sitting on floor in classroom

Stay well (vaccines are on their way)! 


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