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global vaccines given line graph and global map

January 25, 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) School’s back in session for in person learning in KFL&A, Hasting Prince Edward County and Leeds, Grenville and the Lanark District Health Unit, effective today. (click here)!

2) All about COVID-19 Vaccines: Update on global vaccination programs (click here)results from Canada’s vaccine safety monitoring system (click here) provides reassurance of safety, answers to FAQs about vaccination for people who are on blood thinners, have allergies or are immunosuppressed can be safely vaccinated and updates on Canada’s vaccination program (click here)

3) KHSC received no new COVID-19 patients from Toronto-thus far today 

4) Provincial lockdown order for Ontario: Further proof that it is working! (click here)

5) Ontario’s epidemic is now better controlled with a rate of test positivity of 5.5 and 1958 new cases (click here).

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

7) Canada’s COVID-19 epidemic is improving: 749,341 total cases to date, 4852 new cases today, 61,704 active cases (down from 73,635 last Monday) and 19,137 deaths (a cumulative national case mortality rate of ~1.96%).

8) The COVID-19 global pandemic: Global mortality is 2,131,370 million people with over 99 million cases in the pandemic to date (25.2% from the USA which has only 4% of the world’s population) (click here):


1) School’s back in session for in person learning in KFL&A, Hasting Prince Edward County and Leeds, Grenville and Lanark District Health Unit effective today. (click here)!

Because of favorable COVID-19 epidemiology, which directly relates to adherence with public health policies, school is back in session for in person classes for 7 Ontario counties, including those in South Eastern Ontario. There are many happy kids and relieved parents today in Kingston!

2) All about COVID-19 Vaccines: Update on global vaccination programs (click here), results from Canada’s vaccine safety monitoring system provides reassurance of safety (click here), answers to FAQs about vaccination for people who are on blood thinners, have allergies or are immunosuppressed can be safely vaccinated and updates on Canada’s vaccination program (click here)

Here is a snapshot on how we are doing globally in administering vaccine (read out is vaccine/100 people).Israel is doing the best and Canada is in the middle of the pack)(click here)

graphs and a world map showing vaccines doses administered

Global vaccine progress, Jan 25th 2021

COVID-19 vaccines are in general safe. 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 daily by the government of Canada. Here is what we have seen to date (click here):

table giving data on vaccines benefits outweighing the risks

Overall the vaccines in Canada are safe with only 27 serious adverse reactions in the >600,000 vaccines administered to date (and on fatalities).

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

FAQ 1) 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 re patients on blood thinners and the covid-19 vaccine

FAQ 2) 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 summarised 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 nonserious.

logo for Disease control and prevention Morbidity and Mortality weekly report MMWR

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 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)*

The table in blue below offers advice from the CDC on the issue of allergies and vaccines (see below). This is a reasonable approach and suggests careful monitoring for allergic response post vaccination; rather than avoidance of vaccination for most people with allergies.

table providing CDC advice re allergies and vaccines

FAQ 3) 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.

statement re vaccines for patients who are immunocompromised or immunosuppressed

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).

ppt slide on an overhead screenpresenter at podium giving talk with overhead screen behind him showing ppt slides

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 4: 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.

syringe and needle drawing vaccine from a bottle

Vaccination roll-out update (click here): The roll out is moving along but encountering logistical challenges and supply chain problems (notably Pfizer stopping vaccine supply entirely this week and then reducing supply for a month as it retools a factory in Belgium). To date we have not had to deal much with people declining vaccines; rather we are dealing with a pent up demand for vaccines that far exceeds supply. Mr. Trudeau has indicated all Canadians who wish to be vaccinated will be vaccinated by September (click here). 

As of 9:39 CST today a total, 1,122,450 doses of COVID-19 vaccines (including both Moderna and Pfizer-BioNTech) have been delivered and 73.3% of delivered doses have been administered. The Pfizer-BioNTech and Moderna vaccines require two doses, a number of weeks apart. As of today, the vaccine tracker reports that 726,368 Canadians have received at least one dose of an approved COVID-19 vaccine (see below). At least 96,256 Canadians are fully vaccinated, having received both required doses (click here).

map of Canada with each province having a red number in it denoting the vaccine doses administered so far

There is some interesting sociology afoot in Canada’s COVID-19 pandemic with four broad groups of people, as defined by their approach to vaccination. People seem to be in one of four groups. First, there is the majority, who are largely grateful for the vaccine and are impatient with the wait for vaccination. Second, there are vaccine deniers who believe the vaccine is part of some large plot and/or strongly believe that the vaccines are untested and dangerous. They are a diverse and often angry group who are hard to convince. Their views appear to be stoked by a general distrust of government and establishments (including the medical profession). They often refute expert opinions, believing that “experts disagree”, a view promulgated by the media that they consume. A third group has also emerged: vaccine queue jumpers: people who misrepresent themselves to get early access to the vaccines and bypass protocols (such as the one in Ontario that prioritizes vaccination of people in LTCs) (click here). Cheating the queue may land a person in the newspapers or worse. Finally, there is a 4th group, people who are flying south to try and get American vaccines (click here). This is a bit tone-deaf (in my view) as the US government is struggling mightily under the new administration to get its vaccine program up to speed for its own residents and citizens. Many Americans are less than thrilled with visitors taking “their vaccines” (click here). It is likely unwise to travel south just for a vaccine. Canadians may not be able to easily get back on short notice and may be at substantial risk (at least financially) if they get sick while traveling abroad. The government may soon make return to Canada from elective travel more difficult. The policy for returning Canadians is as follows (click here) and requires a negative COVID-19 test:

Starting January 6, 2021 at 11:59 PM EST, air travellers 5 years of age or older travelling to Canada are required to provide proof of a negative COVID-19 molecular test taken, at their own expense, no more than 72 hours before the aircraft's initial scheduled departure time. Travellers who cannot provide proof of a negative test, or who test positive, will not be allowed to board, with limited exceptions. Canadians who are planning to travel abroad should consider how they will meet these requirements before departure, and make plans for the possibility of needing to extend their stay. Travellers who receive a negative test result and are authorized to enter Canada must still complete the full, mandatory 14-day quarantine

3) KHSC received no new COVID-19 patients from Toronto-thus far today 

We remain on standby to receive patients from Toronto but no cases arrived over the weekend or as of noon today. Hopefully with a new MacKenzie hospital opening in Vaughan (click here) and flattening of the provincial COVID-19 curve transfers will not occur in large numbers. 

4) Provincial lockdown order for Ontario: Further proof that it is working! (click here)

New Ontario lockdown rules (see last note), intensified a lockdown which began Dec 26th. These data (form a nice CBC website) shows clear evidence this lock-down is reducing new cases. The graph below shows a decline in new cases in Ontario, coincident with the post-Christmas lockdown. However, with most Ontarians unvaccinated and with no natural immunity we remain susceptible to infection as we reopen (and reopen we must). The reopening post lockdown will require accelerated vaccination and continue good public health practices.

graph showing trends of cases, deaths and hospitalizations in Ontario in last week

Evidence that the post-Christmas lockdown in Ontario is working: a sustained decline in new cases

5) Ontario’s epidemic is better controlled with a rate of test positivity of 5.5 and 1958 new cases (click here).Ontario has had 256,960 COVID-19 cases, 1958 new cases since yesterday (a continued decline and the first time in over a month below 2000 new cases). Our provincial positive COVID-19 test rate remains high at 5.5% today. However, our Re value is 0.87, the lowest since fall 2020, meaning viral spread is being contained. Ontario’s cumulative provincial COVID-19 rate is 1728.7/100,000 population, 5-times higher than in KFL&A (304.6 cases/100,000 population).

table with current pandemic numbers at a glance

Ontario’s pandemic at a glance: Jan 25th, 2021 (click here)

map of Ontario colour coded depending on number of cases / 100,000

Most of Ontario’s regions report more than 40 cases of COVID-19/100,000 population in the past 2 weeks (red in map above)

Peel (on Toronto’s western border) remains the hot spot in Ontario with 3269.5.9 cases/100,000 population, as measured form the beginning of the pandemic (click here). However, a look at recent infections (infections within the past 2 weeks, expressed as cases/100,000 population) puts Windsor in the unenviable spot, once again, as being the leading site of infection:

Rate of cases/100,000 population in the past 2 weeks






Cornwall: 241

photo of CN tower and Torontos waterfront and skyline

Although COVID-19 is increasing in Toronto as a whole, case load is widely variable 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 7,288 cases/100,000 residents, ~ 10X the burden of COVID-19 in the Runnymeade-Bloor West Village neighbourhood (715 cases of COVID-19/100,000 residents). When one examines recent cases, since Jan 1st 2021, case prevalence is still high-ranging from 72 cases/100,000 residents in Mount Pleasant East to 1319 cases/100,000 residents, in Humbermede (click here).

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

6) 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 is now 661, not counting the prison outbreak. This is up 16 cases since last Thursday. Admittedly these data are from yesterday, when the website was last updated. There has only been one death of a KFL&A resident since the pandemic began. There are 18 active cases in the community, down markedly from the 52 active cases 2 weeks agoThere are 3 COVID-19 patient hospitalized at KGH (down from 5 last week).

table with graphs, maps and numbers detailing covid -19 data for KFL&A

COVID-19 rates remain low in KFL&A

Testing: There remains a need for genomic surveillance to detect viral mutations. The mutations to date all appear to be susceptible to vaccine protection. However the N501.V2 mutation (initially found in the UK) seems to be more infectious, especially amongst young children (stay tuned). It is highly likely to be vaccine sensitive (click here). This variant was imported into a nursing home in Barrie Ontario (click here), Roberta Place, and has infected 127 residents and 84 staff and led to 27 deaths.  Hopefully this outbreak can be contained. The E484K variant found in South Africa, Brazil and Japan is still being studied to ensure that it does not have immune evasion capacity (click here).

photo of Prime Minister Boris Johnson (UK) at podium with two UK flags behind him delivering speech

SARS-CoV2 variant devastates Barrie nursing home

Bottom line: The vaccine will ultimately protect us; however, it will take months to get a critical mass of Canadians vaccinated. Meanwhile we have to rely on good public health practices. This is the final leg of a marathon and the next 3-4 months will challenge us all to remain patient and follow policies that we acknowledge have harsh financial and social consequences. We are in a race against new viral variants that seem even more adept at infecting us. However, there is light at the end of the tunnel in the form of the vaccines.

photo of B&W railway tunnel with a daylight at the end

7) Canada’s COVID-19 epidemic is improving: 749,341 total cases to date, 4852 new cases today, 61,704 active cases (down from 73,635 last Monday)and 19,137 deaths (a cumulative national case mortality rate of ~1.96%). Our second wave of COVID-19 (orange line-top panel below) has reached a plateau and after a week or two of decline in case numbers we are now seeing the expected fall in hospitalizations (gold graph, bottom left). 89.1% of all cases have already recovered. There has been a 1.96% national mortality rate amongst people diagnosed with COVID-19 (see below). 

bar graphs on the left and line graphs middle and right showing 2nd wave covid data in Canada

COVID-19 in Canada: Wave 2 hospitalizations beginning to decline -Jan 25th, 2021 

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 resumed a plateau trajectory. Rates in Ontario and Quebec (home to almost 63% of all Canadians) appear to have hit a plateau and have begun to decline. Rates of new infection have remained high in New Brunswick, mostly in norther NB, (see below) but 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.

line graph showing increase in cases in New Brunswick

Active cases (orange line) have yet to plateau in New Brunswick

8) The COVID-19 global pandemic: Global mortality is 2,131,370 million people with over 99 million cases in the pandemic to date (25.2% from the USA which has only 4% of the world’s population) (click here):

There has been a total of 2,131,370million deaths and 99,283,370 million cases since the pandemic began.The number of cases has increased >6-fold since early August, 2020, when there were 16 million cases. The pandemic hot spots are in the USA, India, Brazil, and Russia, with the UK, France and Turkey in hot pursuit! (click here). A positive note is an apparent plateauing of active cases (see bottom right orange graph).

ranking of countries with highest covid on left, global map in centre with pink dots and ranking of countries deaths and recovered far right

Global COVID-19: New cases may have peaked (bottom right): Jan 25th 2021

The USA with 25,137,632 cases and 419,228 deaths tops the COVID-19 list and accounts for ~25.3% 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 and Russia combined! The COVID-19 active case map (above) shows the high incidence of active infections in the US and South America, as well as in Europe (the bigger the salmon-colored dot the higher the active cases/100,000 population). The ONLY solutions to this are adherence to public health measures and rapid, mass vaccination.

Improving USA positive test rates and extension of border closure (click here): The USA has seen a modest improvement in positive test rate of 9.0% (click here) (see below). California has a positive test rate has also decreased to 8.1% whilst South Dakota remains at a staggering 27.6% rate of test positivity today. For snowbirds: rates in Florida remain high (10.3% today)-see below. 

line graph

Improvement in positive test rates in the USA

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 requirements, including quarantine) (click here).

land border bridge with USA and Cdn flags

Regular reminders

KHSC bed capacityBed capacity has increased to 96 beds (up from 71 beds last Thursday) (see graphic below). Our ventilator supply remains good; however, critical care beds are in short supply (see below); albeit better than last week. 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!

bar graphs

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.

finger scrolling on iPhone

KHSC visitor policy: 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 and this family presence policy will be updated by the end of the week (to make it clear who grants final decisions on exceptions that allow access). 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. 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). The Beechgrove Complex is south of the King St. West/Portsmouth Avenue intersection. Signage will direct people through the Complex to the Recreation Centre building at 51 Heakes Lane for walk-in testing. 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 receiving covid 19 nasal swab and showing how far the swab goes into the nasal cavitythree young boys dressed up as doctors with their arms crossed 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 3,336 deaths in nursing homes (up 80 deaths since Monday) account for ~58% of all deaths in Ontario, click here. There are also ~ 1253 active cases in LTC residents and 1196 active cases in LTC staff! In the last month the rate of death amongst LTC residents has continued to increase daily and is now >100/week! 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. 

table with current COVID 19 data in LTC in Ontario

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. Below is the new baseline report for school age children in publicly funded Ontario schools. School boards report every weekday from Monday to Friday.

table of covid data in school related cases

Here are the parallel data from licensed child care facilities in Ontario.

table of COVID data in licensed child care facilities

Thoughts on political censorship and science from Dr. Deborah Birx-for your interest (click here): Dr Deborah Birx, appointed by Mr. Obama to lead the government response to AIDS and kept on by Mr. Trump to lead the fight against COVID-19, was interviewed on CBS news. She discusses the challenges she faced dealing with scientific interference by the government, the cost to her reputation of adhering to the chain of command and she explains why she stayed on, despite criticism from Republicans and Democrats alike. Her case illustrates the high price of trying to improve the American COVID-19 response while being systemically undermined by political actors. It is a useful lesson for Canadian governments and healthcare systems and reminds us of the importance of letting scientists speak without censorship. Whatever one thinks of Dr. Birx, the price she paid for her commitment to improve healthcare merits a listen. 

screenshot of women sitting in a chair on face the nation

Stay well!


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