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flow chart showing testing process with test tubes

May 27, 2020 - Dr. Archer's Update on COVID-19 response from the DOM and Medicine Program

COVID-19 Update: There is little change in the fortunate situation in the Kingston, Frontenac Lennox and Addington (KFL&A) region with ~220,000 residents. There are no new cases of COVID-19 today (see update from KFL&S Public Health). The positive test rate in KFL&A remains at 0.6% (vs 4.2% in Ontario). The running total for the epidemic remains at 62 COVID-19 cases in the KFL&A region and all infected people have now recovered. Our PPE supply is stable with 3 weeks reserve, at the current level of activity. 

One issue that is emerging as we deal with the increasing testing of asymptomatic people is that the nasal swab PCR test does not work as well in these individuals. There are two challenges in healthy people, one being sample acquisition and the other being viral load. 

1) Health nasal mucosa often yields little mucus or cellular material, so there is no RNA/DNA to amplify in the PCR assay (the genetic test used to measure the presence of virus-see image below). These tests come back neither positive nor negative; rather they are reported as PSQ (poor sample quality). PSQ tests are rare in symptomatic people but now account for up to 10% of all swabs in asymptomatic people.

2) If a person actually is very early in a COVID-19 infection their viral burden may still be so low as to be undetectable (even though they will ultimately have more virus and become detectable). This accounts for a low negative predictive value for the test (70%). In contrast, when people have symptoms (cough, fever etc) a negative test truly means no COVID-19 infection with 98% confidence (for our KHSC lab). If you always wanted to be a molecular biologist, here is a diagram of how we do PCR to detect viral genes.

flow chart of how PCR is done showing test tubes

Cartoon showing how labs can change RNA to DNA and then use a polymerase chain reaction (PCR) technology to amplify the tiny signal and use fluorescent probes to measure how many copies of the viral genes were present in the sample. At KHSC our lab measures 2 SARS-CoV-2 viral genes and 1 reporter gene which serves as a standard (image copied from source)

Kingston remains in a bubble with a low incidence of COVID-19 (28.7 cases/100,000 population), positioning us to carefully reopen the city and ramp up activity at KHSC and Queen’s University (read the blog if you’re interested in hearing more re: Queen’s). In contrast Toronto has a rate 10 times higher (306.2 cases/100,000 population). The Toronto incidence has been rising over the past week. This is a reminder that the pandemic varies in impact greatly by location. Nonetheless, as the graph for Ontario shows, the number of new cases is decreasing (i.e. the curve is flattening).

graph of COVID-19 cases in Ontario by date

It’s good to be young: I would like to address the issue of COVID-19 disease in young people. While it may be too early to exclude a significant impact on children the Ontario data are fairly compelling on two points.

Picture of baby Yoda
  1. Detected COVID-19 infections largely occur in adults. This may not mean that children are not infected; rather they may simply handle the infection well and largely remain asymptomatic. Alternatively, they may be less susceptible to infection.
graph of COVID-19 cases in Ontario by age group

2) The mortality from COVID-91 is clearly mostly in the elderly. The older (and/or frailer) one is the worse the prognosis. See below a graph of death from COVID-19 by age in Ontario.

graph of COVID-19 deaths in Ontario by age group

How’s the epidemic going? To date there have been 86,939 cases of COVID-19 and 6671 deaths in Canada (see below), which is minimally changed from yesterday! Most cases of late are acquired from community contact and/or close contact (circle graph below). Nationally, the COVID-19 curve has flattened, with a decline in the number of new cases (see bar graph below, right). 

by the numbers pic of cover-19 in Canada

COVID-19 continues to disproportionately affect the elderly and particularly the frail residents of long term care facilities (LTC) (see today’s data below). The ~78,000 residents of Ontario’s LTC facilities account for less than 0.5% of the population but they account for ~72.4% of all deaths from COVID-19! There has been continued increases in deaths in our LTC facilities in Ontario with 49 deaths since yesterday!

chart summarizing LTC cases of COVID-19 in Ontario

It will be interesting whether this human tragedy will result in true system reform and/or criminal charges (click here).

screenshot of Doug Ford addressing LTC and military scathing reports

Testing for SARS-CoV-2: We have tested 4.25 % of all Canadians (1,550,549 people) and are at the same rate of testing in Ontario (4.35%). The rate of testing remains low in Ontario of late because there are fewer people with respiratory tract infection symptoms of cough and fever (and thus there has been less call to be tested). 

graph showing Canada tests performed vs positives

To see where Canada stands amongst nations in the COVID-19 pandemicclick here. The global case total has risen to 5,626,047 with 351,815 deaths. America still has more cases (1,671,728) than the next 9 most affect countries combined! Here is a list of the countries with over 100,000 reported cases of COVID-19.

chart showing confirmed deaths by country/regionalarm clock with smiley face

A revised reminder for people in the community 

1) People in the community can self-refer for assessment and possible testing. We are now on testing people for much broader indications (we are no longer requiring fever or travel as preconditions for testing). We are now testing people who have only 1 COVID-19-type symptom or who are concerned they have been exposed to the disease. KFL&A has also suggested that health care workers should be routinely and repeatedly surveyed by nasal swabs (discussed above). You can seek out testing at Memorial Centre in Kingston, (see instructions below). Here is a link to the self-assessment tool used to see if you should be tested (although I suspect it will be updated soon): click here. (last updated May 19th)

COVID-19 self assessment instructions

The Community COVID-19 Assessment Centre is located at:
Kingston Memorial Centre (please use the well-marked main entrance) 
303 York Street, Kingston, Ontario 
Monday to Friday: 10:00 a.m. - 6:00 p.m.
Saturday and Sunday: 9:00 a.m. - 12:30 p.m. 

2) Our hospitals and clinics are safe places to receive care (in part because everyone including staff is screened prior to entry and in part because the local incidence of COVID-19 remains low). You should not delay accessing care that you or your doctor deem to be urgent.

Your moment of Zen: COVID-19 has provoked changes to all our lives an periodic stress relievers are welcome. Here is a lovely photo of a scarlet taninger from a friend, Mr. Ted Dyke. Enjoy his amazing photography!

photo of a red bird with black wing perched on a tree branch

Here are some iPhone pics from me-a celebration of the beauty of spring in Kingston.

photo of white flowersphoto of purple lilac treephoto of 2 swans swimming in lakephoto of a young fox

Stay well!

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