COVID-19 and Vitamin-D

The chart above shows national Covid mortality against latitude of national capitals (open circles are for the Southern Hemisphere, solid circles for the Northern). The trend line in blue has a correlation of 0.50 (with p < 10−13). Countries further away from the equator are definitely reporting more Covid deaths.

It is possible that these numbers reflect under-counting in the tropics (although this is unlikely for Singapore = SG) and over-counting in wealthier countries away from the tropics (e.g. by reporting deaths of patients with positive Covid tests as Covid deaths, even if the actual cause of death is unrelated). However, it seems unlikely that under-counting and over-counting can explain everything here.

This paper in The Lancet notes that “It has long been clear that groups that traditionally exhibit vitamin D deficiency or insufficiency, such as older adults and nursing home residents, and Black, Asian, and minority ethnic populations, are the same groups that have also been disproportionately impacted by COVID-19. Additionally, increased time spent indoors due to strict lockdowns and shielding triggered concerns that some people might not obtain the necessary physiological levels of vitamin D from sunlight.

My chart above is consistent with this: decreased sunshine away from the equator appears to increase Covid mortality, presumably due to vitamin D deficiency. This study in QJM notes, “vitamin D supplementation is effective in reducing COVID-19 severity. Hence vitamin D should be recommended as an adjuvant therapy for COVID-19.” Personally, I have been taking this advice for quite some time.


COVID-19 in the UK #4

The chart above (click to zoom) is an updated view of registered deaths in England and Wales according to the ONS up to the end of the year, along with data from previous years.

The difference between the red and black lines (highlighted in yellow and labelled A) indicates deaths where COVID-19 was mentioned on the death certificate.

There was also a spike in non-COVID-19 deaths (labelled B), which seems to reflect under-treatment of cancer and other serious diseases during the lockdown. The Telegraph expressed concern at this some time ago, and I myself know people in this tragic category.

For a while (label C) deaths were actually running slightly below trend, but deaths unrelated to COVID-19 then increased again, perhaps due to the renewed lockdown. More recently, there are now indications of a “second wave” of COVID-19, with a slight increase in deaths where COVID-19 was mentioned on the death certificate (labelled D). However, the increase is significantly slower than the first wave, and (given the dip in the red line) some of these reported COVID-19 deaths may be misdiagnosed seasonal influenza. The overall death rate at the end of the year was much the same as for previous years.

The bar chart at the bottom shows a year-to-date comparison with previous years. The white additions to the bars for previous years show an adjustment to account for population growth.


COVID-19 in the UK #3

The chart above (click to zoom) is an updated view of registered deaths in England and Wales according to the ONS up to 4 September, along with data from previous years.

The difference between the red and black lines (highlighted in yellow and labelled A) indicates deaths where COVID-19 was mentioned on the death certificate. The scale of the deaths is sobering, although the worst seems to be over.

There was also a spike in non-COVID-19 deaths (labelled B), which seems to reflect under-treatment of cancer and other serious diseases during the lockdown. The Telegraph expressed concern at this some time ago, and I myself know people in this tragic category. Hopefully, things will be handled better the next time there is an epidemic

Recent deaths (labelled C) have been running slightly below trend, presumably because some of the vulnerable people in the community who would have died about now are already dead.

The bar chart at the bottom shows a year-to-date comparison with previous years. The white additions to the bars for previous years show an adjustment to account for population growth.


COVID-19 in the UK #2

The chart above (click to zoom) is an updated view of registered deaths in England and Wales according to the ONS up to 26 June. The difference between the red and black lines (highlighted in yellow) indicates deaths where COVID-19 was mentioned on the death certificate. The red line shows that a spike in non-COVID-19 deaths also took place.

Sombre news, but the COVID-19 peak seems to have passed.

Edit 1: Updated chart for more recent data.

Edit 2: The Telegraph is expressing concern at the spike in non-COVID-19 deaths, which seems to reflect under-treatment of cancer and other serious diseases during the lockdown.


COVID-19 in the UK

The chart above (click to zoom) shows registered deaths in the UK according to the ONS up to 10 April (note that during holiday periods, some deaths may be “carried over” to the next week). The year 2020 is on the way to passing 2018 as the worst year of recent times, with the fortnight to 10 April being particularly bad.

The difference between the red and black lines (highlighted in yellow) indicates deaths where COVID-19 was mentioned on the death certificate (this includes deaths “with” as well as “from” COVID-19, although other data suggests that in most cases COVID-19 would be the actual cause of death). A clear COVID-19 spike is visible.

The jump in the red line is also disturbing, however. The the red line shows deaths excluding deaths where COVID-19 was mentioned on the death certificate. The jump in the red line may indicate:

  • COVID-19 deaths where no test was done (unlikely, because the records show only a slight increase in deaths by non-COVID respiratory illness); or
  • deaths from other causes exacerbated by lack of hospital beds; or
  • deaths due to the current lockdown itself (e.g. suicides).

At present, I have no way of deciding which of those three options are the correct ones. Hopefully both COVID-19 and those other factors will pass soon (the IHME model suggests that COVID-19 deaths in the UK reached their peak on 21 April).

I should note that CNBC has also looked at this dataset, but they’ve compared this year against an average period that excludes 2018 and 2019. I don’t know why they did that.


Visualising COVID-19 risk

A friend suggested this to me as a way of visualising COVID-19 risk for the United States. The red bars in the chart above show the expected death rates for different age groups over the whole pandemic period up to August 2020 (combining the projected total deaths from IHME with the age breakdown from CDC). For comparison, the blue bars show the expected deaths from other causes over an ordinary 9-day period (using data from CDC). For every age group, the risk of dying from COVID-19 during the pandemic is less than 9 days worth of ordinary risk, because 7,700 people die in the United States on an average day (of course, the COVID-19 risk would be somewhat higher without current social distancing measures).

For children and young people aged 0–24, the risk is less than 1 day worth of ordinary risk. This is clearer if we re-plot the chart on a logarithmic scale:

Update: I have updated the charts above to match the new IHME projections dated 16 April.


COVID-19 projections

This web site has been making COVID-19 projections for the US that seem to be tracking reality fairly well. They are predicting that 0.018% of the US will die. Comparing with this list, that is about 8% more than are normally killed during a year by ordinary influenza or pneumonia.

The apparent high death rate in other countries seems to be due to a combination of poor-quality health care and inflated statistics resulting from under-testing the population. In a few weeks, we will see how accurate the US projections are (the Wyoming predictions seem dubious to me).

Below, from the same projections, are predicted ICU bed demands in excess of state capacity (click to zoom). It can be seen that there is a particular problem in the northeast.

Update: I have updated the charts to match the new IHME projections dated 16 April, and added expected death rates for each state (below, click to zoom):

The expected death rates for each state seem to have no relationship to the number of control interventions implemented by state governments. Clearly other factors are decisive:


Some principles of network epidemiology

Lockdowns and “flattening the curve” are very much in the news right now, so I thought it was timely to post about some principles of network epidemiology. The charts below (click to zoom) show the simulated spread of a disease (in a small “toy” population of 2000) subject to certain assumptions. The blue lines show the total number of cases over time (adding up those infected, recovered, and dead). This total number is important because some percentage of the final total will die, and we want to minimise that (if we can). The red lines show the number of current infections over time. This is important because some percentage of the red numbers are in hospital, and the red peak therefore represents peak load on the medical system.

In the top row, we have connections happening at random, with increasing social distancing happening from left to right. Moderate social distancing doesn’t change the fact that almost everybody gets the disease, but it does delay and reduce the peak, thus taking strain off the medical system. Extreme social distancing saves many lives, but only if social distancing is continued for a long time (in real terms, until a vaccine is available, which is almost certainly not sustainable).

In the middle row, we have the same number of contacts happening as in the top row, but most of the contacts are within limited social circles. Such contacts, between family members and close friends, are less serious than contacts with strangers. If Peter is your close friend, and you catch the virus, then there’s a reasonable chance that Peter caught it the same way, and so there’s a reasonable chance that your contact with Peter makes no actual difference. If Peter is a spouse, child, or flatmate, that’s quite a good chance. Contacts with strangers, however, can spread the disease from one social circle to another, and so are far more serious.

In the bottom row, we again have the same total number of contacts happening, but a few “super spreaders” have many more contacts than average (while the majority have slightly less than average, to compensate). This third scenario is significantly worse than the top row – higher, earlier, red peaks, and many deaths even when there is extreme social distancing. Unfortunately, experience has shown that medical personnel, in spite of the fantastic work that they do, have the potential to be serious “super spreaders,” because:

  • they have contact with many patients;
  • the patients are strangers; and
  • the patients are more likely than average to be elderly and/or vulnerable.

This is why personal protective equipment (PPE) for medical personnel is so critically important, as are good testing protocols for medical personnel. Other kinds of “super spreaders” also occur, of course, and it is important to identify them, test them, and provide them PPE (or stop them doing what they’re doing, if it’s non-essential – some jurisdictions with supposedly strict rules are still allowing prostitutes to operate, for example).

Overall, if we look at columns in the picture (all three charts in each column have the same total number of contacts), we see that the kind of contact is just as important as the number of contacts. Isolation regulations in some jurisdictions don’t always recognise that fact, unfortunately.


Coronavirus diary #1

The SARS-CoV-2 coronavirus is changing the world. Ridiculous and selfish panic-buying is stripping supermarket shelves, in Australia as elsewhere. Everyone I know is catching up on their reading, and people are being persuaded to practice social distancing and to wash their hands.

It seems to me that if you’re under 50 and healthy, there is absolutely no need to panic. But it’s really important not to pass on the disease, if and when you catch it, to other people. Listen to your local medical advice, people!

Virus photo from NIAID Rocky Mountain Laboratories; supermarket photo by Christopher Corneschi, 9 March 2020; painting by Marguerite Gérard; hand-washing photo by Michelle Gigante/USAF.


The spread of the COVID-19 coronavirus

Above is a chart of worldwide cases of the COVID-19 coronavirus disease (data from here, skipping the first few days). The apparent spike in cases on February 12 is due to a change in how cases are diagnosed and reported.

There does not seem to be the exponential growth in cases that one would expect (see the badly-fitting blue curve), except at first. In fact, allowing for the “false spike,” growth seems to be almost linear (see the dashed purple line). This would probably be due to under-counting (the Chinese medical system can only diagnose a certain number of cases each day), although it offers some hope that quarantine measures may be working. Let us pray that they continue to work.