Covid-19 – Comparing Direct Case Measures and Waste-water Estimates (Alberta Canada)
It is now fairly common throughout the world to estimate the “true” level of Covid in a community from analysis of waste-water in municipal sewage systems. People infected with the virus that causes Covid-09 will shed some virus particles in their feces, which can be detected by instrumentation at regular intervals.
The trend in those measures will then give an indication of how many infections are actually active in the community. Not every person who is infected ever gets tested, but they will shed virus particles into the sewage system, so in principle this can be considered a superior method for tracking the true infection rate.
I used the data from Edmonton, Alberta to see how the trend in these
two measures correlated. Note that though this data is from a particular locality, the general conclusions of the analysis would likely hold true in most other locations, as well.
Below is a graph of Covid Cases in Edmonton during the October 2021 to May 2022 period, the times for which waste-water analysis is available on the Alberta government website. The left y-axis shows Edmonton region Covid cases (in yellow), while the right y-axis gives Covid Cases per Millilitre of waste-water in the combined Edmonton and Fort Saskatchewan waste-water treatment plants, the two plants that handle the bulk of the metro area’s waste-water.
As you can see, there is a good correlation for much of the period (the two lines almost overlay each other), though that relationship breaks down in the latter half of the period.
The waste-water measures are not taken every day, The data for direct case measures have some jitter as well (case counts are affected by the cycle of weekdays and weekends). Therefore, I constructed another graph with this data, using a seven-day moving average for both measures and lagging direct case measures by two days, relative to waste-water measures (it takes some time to actually get tested after symptoms begin). Two days was the amount of time that had the highest correlation between case counts and waste-water measures.
As noted, the nice visual correlations between the two lines in the line graphs break down at about the mid-January period of 2022. This effect is perhaps even better seen in the third graph, a scatter-plot of waste-water measure vs Covid case counts.
That graph shows that the relationship between the waste-water measures and the case counts is very similar for the Delta (blue, Oct21 to mid-Dec22) and Omicron.BA1 (red, mid-Dec21 to mid-Feb 22) periods, but much different for the Omicron.BA2 period (yellow, mid-Feb22 to May22). During that latter period, the slope of the regression line is much shallower than in the other two periods. In other words, any given measure of Covid copies per millilitre of waste-water corresponds to far fewer Covid cases during the Omicron.BA2 period that it did in the earlier phases.
The regression results are given below, or can be read directly off the graph. I used the “force y-intercept to 0” option, as it makes sense that when the waste-water results are at or near 0, the covid cases will also be at or near 0. For various reasons (e.g. lag times, measurement error, dis-interest in getting tested) that won’t be exactly true, but it should be reasonably close.
Waste-water (X) vs Covid (Y)
Forcing y-intercept to 0 beta coeff R2 Ratio(Delta)
Delta (Oct 21 – mid-Dec 21) 2.43 0.94 1.00
OmicronBA1 (mid-Dec 21 – mid-Feb 22) 2.18 0.91 0.90
OmicronBA2 (mid-Feb 22 – May 22) 0.71 0.96 0.29
These figures can be interpreted as:
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Beta coefficient – gives the number of cases expected for each increase in the Covid copies per millilitre of waste-water.
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R2 – shows how close the fit is to a straight line, with numbers closer to 1 indicating a better fit.
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Ratio – shows how the other periods in question compare to the Delta variant period. So, for example, the Omicron.BA2 period had less than one-third as many cases for a given waste-water measure than did Delta.
It seems reasonable to assume that the Delta period gives the best measure of the relationship between the waste-water results and Covid counts and thereby Covid infections (though counts would have under-represented infections even then). That’s because Covid counts were relatively low during that period, so the medical system would not have been swamped by high demand for testing. In other words, a fairly high proportion of people with Covid symptoms would have likely gone on to be tested, and thus have been included in official case counts.
So, it seems that Covid numbers were probably becoming more and more seriously under-counted as the first wave of Omicron.BA1 progressed. This seems to have worsened during 2022, such that the Covid case count was likely very far off the true figures.
Why might that be? Here are some hypotheses:
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The rapid sequence of Omicron.BA1 followed by Omicron.BA2 may have overwhelmed the testing system, resulting in a smaller proportion of infected people actually getting tested as time went on. Thus, the relationship between the waste-water measures and case counts became shallower.
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With the growing sense within the population that Covid isn’t as pathogenic as it first was, many people might have decided not to bother with seeing a doctor or going to a clinic, as they felt they could just let the disease run its course.
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The Alberta government had provided free home-testing kits fairly early in the first Omicron wave. As time went on, these kits were used up, and people decided not to bother with the home-testing if they had to purchase the kits themselves. Thus, testing declined.
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Omicron.BA2 may have some odd effect, whereby infected people shed virus particles into the sewage system at a much higher rate than the other variants. While this may be true, it seems unlikely, as there has been no indication of that published, at least of which I am aware.
So, essentially, the waste-water results indicate that the number of Covid cases is probably now being vastly under-counted. One problem with that is that it may be giving the impression that Omicron.BA2 is more pathogenic than it really is. That’s because deaths will still be fairly reliably counted, while case counts become a less and less measure of actual infections.
I will see what the data says about that in a future blog.
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And, here’s are some travel books to peruse, now that the reduction in Covid cases and severity has opened up travel again (fingers crossed).
A Drive Across Newfoundland
U.S.: https://www.amazon.com/dp/B07NMR9WM8
U.K.: https://www.amazon.co.uk/dp/B07NMR9WM8
Germany: https://www.amazon.de/dp/B07NMR9WM8
Japan: https://www.amazon.co.jp/dp/B07NMR9WM8
Canada: https://www.amazon.ca/dp/B07NMR9WM8
Australia:https://www.amazon.com.au/dp/B07NMR9WM8
India: https://www.amazon.in/dp/B07NMR9WM8
Newfoundland, Canada’s most easterly province, is a region that is both fascinating in its unique culture and amazing in its vistas of stark beauty. The weather is often wild, with coastal regions known for steep cliffs and crashing waves (though tranquil beaches exist too). The inland areas are primarily Precambrian shield, dominated by forests, rivers, rock formations, and abundant wildlife. The province also features some of the Earth’s most remarkable geology, notably The Tablelands, where the mantle rocks of the Earth’s interior have been exposed at the surface, permitting one to explore an almost alien landscape, an opportunity available on only a few scattered regions of the planet.
The city of St. John’s is one of Canada’s most unique urban
areas, with a population that maintains many old traditions and
cultural aspects of the British Isles. That’s true of the rest of
the province, as well, where the people are friendly and inclined to
chat amiably with visitors. Plus, they talk with amusing accents and
party hard, so what’s not to like?
This account focusses
on a two-week road trip in October 2007, from St. John’s in the
southeast, to L’Anse aux Meadows in the far northwest, the only
known Viking settlement in North America. It also features a day hike
visit to The Tablelands, a remarkable and majestic geological
feature. Even those who don’t normally consider themselves very
interested in geology will find themselves awe-struck by these
other-worldly landscapes.
A Ride on the Kettle Valley Rail Trail: A Biking Journal Kindle Edition
by Dale Olausen (Author), Helena Puumala (Editor)
The Kettle Valley Rail Trail is one of the longest and most scenic biking and hiking trails in Canada. It covers a good stretch of the south-central interior of British Columbia, about 600 kilometers of scenic countryside. British Columbia is one of the most beautiful areas of Canada, which is itself a beautiful country, ideal for those who appreciate natural splendour and achievable adventure in the great outdoors.
The trail passes through a great variety of geographical and geological regions, from mountains to valleys, along scenic lakes and rivers, to dry near-desert condition grasslands. It often features towering canyons, spanned by a combination of high trestle bridges and long tunnels, as it passes through wild, unpopulated country. At other times, it remains quite low, in populated valleys, alongside spectacular water features such as beautiful Lake Okanagan, an area that is home to hundreds of vineyards, as well as other civilized comforts.
The trail is a nice test of one’s physical fitness, as well as one’s wits and adaptability, as much of it does travel through true wilderness. The views are spectacular, the wildlife is plentiful and the people are friendly. What more could one ask for?
What follows is a journal of two summers of adventure, biking most of the trail in the late 1990s. It is about 33,000 words in length (2 to 3 hours reading), and contains numerous photographs of the trail. There are also sections containing a brief history of the trail, geology, flora and fauna, and associated information.
After reading this account, you should have a good sense of whether the trail is right for you. If you do decide to ride the trail, it will be an experience you will never forget.
Amazon U.S.: https://www.amazon.com/dp/B01GBG8JE0
Amazon U.K.: https://www.amazon.co.uk/dp/B01GBG8JE0
Amazon Germany: https://www.amazon.de/dp/B01GBG8JE0
Amazon Canada: https://www.amazon.ca/dp/B01GBG8JE0
Amazon Australia: https://www.amazon.com.au/dp/B01GBG8JE0
On the Road with Bronco Billy
Amazon U.S.:http://www.amazon.com/gp/product/B00X2IRHSK
Amazon U.K.: http://www.amazon.co.uk/gp/product/B00X2IRHSK
Amazon Germany: http://www.amazon.de/gp/product/B00X2IRHSK
Amazon Canada: http://www.amazon.ca/gp/product/B00X2IRHSK
