Wednesday 26 October 2022

Monkeypox vs Covid – DNA vs RNA (The First 168 Days)

The first months of the global Covid-19 and Monkeypox outbreaks provide an interesting contrast. The graphs below demonstrate those differences.

Comparison of Covid-19 and Monkeypox Cases over Time

The graph below is a straight-up gives a straight-up comparison of the raw data for the first 168 days for the two diseases (the red (Covid Total Cases) and green (Monkeypox total cases) lines). Looking at it this way, there is little similarity between the two; Covid-19 was a much more extreme outbreak in its initial phase than Monkeypox has been up to this point in time.

However, this is somewhat misleading, as Monkeypox has been confined almost entirely to a small demographic group, defined as men who have sex with men (MSM), while Covid-19 cases were widespread, occurring in fairly equal proportions in most demographic groups (e.g. gender, age, etc. groups). So, to get a sense of how a Monkeypox outbreak might develop if it were to cross over to the general population, an adjustment has been made. The resulting hypothetical data is shown in the yellow line (Monkeypox Adj Cases for Full Pop).

To make this adjustment, a few assumptions were make:

MSM are males.
MSM make up about 3 percent of the male population, or about 1.5% of the population in general.
MSM that are at risk of Monkeypox are primarily in the 20 to 59 age groups (the most sexually active group).
To adjust Covid-19 cases to simulate this sub-group, the numbers for the Monkeypox group were divided by 0.015, which produces the Monkeypox adjusted line in the graph.

The next graph shows the data as Covid Cases per Day and Monkeypox Adjusted Cases per Day. Both are converted into 7 day moving averages, in order to smooth out the time series.

In both graphs, it can be seen that the Covid-19 line and the Monkeypox Adjusted line are quite similar up until about Day 100; after that they diverge sharply.

In the Aggregate Cases graph Monkeypox begins to taper off after about Day 100, while Covid-19 continues its exponential rise.
The Cases per Day graph shows some more detail. Both functions rise steadily until about Day 80. They then flatten out until about Day 100. After that, the Monkeypox Cases per Day begins a steady decline, while the Covid-19 cases per day line begins shooting up again, quite rapidly.
I should note that Day 100 for the Covid-19 data being used was April 30, 2020, whereas for Monkeypox it was Oct 21, 2022.

Possible Explanations for the Differences in the Covid-19 and Adjusted Monkeypox Lines

So, what might account for the differences in these two outbreaks?

Covid-19 is an RNA-based virus, whereas Monkeypox is DNA-based. The former are much more susceptible to mutations than are the latter. So, at about the Day 100 to Day 120 time period, it appears as if the Covid-19 virus mutated into a new, more contagious form. That form then out-competed the previous version, as shown by the line on the graph shooting up at that point. And, according to WHO, May 2020 was when the Beta variant of Covid-19 was first identified.
Conversely, Monkeypox, being a DNA-based virus did not have time to mutate. So, the graph took on the somewhat parabolic shape of rise, hit a maximum, then fall. Note that this was a pattern that was often seen in the Covid-19 data (at least in Alberta Canada), just before a new variant will come on the scene. Then, there would be a sudden steep increase, as seen at about Day 120 in the Covid data for this graph. Since Monkeypox is slow to mutate, this rise is not seen in the data for Monkeypox cases.

The fact that Monkeypox was mainly confined to a particular demographic (MSM) also meant that the combination of vaccines and/or behavioral changes could stop and reverse the course of the outbreak, which appears to have happened (e.g. an existing smallpox vaccine is said to be effective against Monkeypox).

Comparison of Deaths from Covid vs Monkeypox

So far, Monkeypox has had a very low fatality rate. As of Day 168, only about 32 people had been recorded as dying from Monkeypox, from a case count of over 75,000. So, that’s only about 42 deaths per one hundred thousand cases. Covid, on the other, had recorded about 536,000 fatalities by day 100, from about 10,500,000 cases, or about 5100 per hundred thousand. That’s a huge difference.

Again, however, we have to account for the difference in at-risk populations, when considering how lethal the two viruses were. Since Monkeypox was mostly confined to the MSM (men who have sex with men) group, we can make the reasonable assumption that the vast majority of these men were in younger age cohorts. We should then compare the Monkeypox Case Fatality Rates with these younger cohorts, bearing in mind that Covid-19 became much more dangerous as the age of the patient increased.

The figures below show some age-based comparisons. I used data from Alberta Canada for this comparison, as the age-based data for that jurisdiction is easily available, and that region seems like it would be quite representative, as about two-thirds of all Monkeypox cases are from western countries, which would have medical and socioeconomic conditions broadly similar to Alberta:

Monkeypox (global): 42 deaths per 100,000.
Covid-19 (Alberta, Canada) ages 20 to 40: 29 deaths per 100,000
Covid-19 (Alberta, Canada) ages 20 to 50: 54 deaths per 100,000
Covid-19 (Alberta, Canada) ages 20 to 60: 118 deaths per 100,000

So, from that point of view, Monekypox is comparable in severity to Covid-19, at least for these age cohorts. This implies that if Monkeypox were to become widespread in the overall population, the effects could be quite severe. Added to that is the fact that Monkeypox has historically been much more severe in children than in other age groups.

Summary

So, in summary, a widespread Monkeypox pandemic would be a bad thing, something that we definitely would want to avoid. Fortunately, however, it does not seem likely to have a high mutation rate, so a widespread Monkeypox pandemic would likely be less of a problem than the Covid-19 pandemic.

Covid-19( SARS-CoV-2) - electron microscope photo

Monkeypox Virus - electron microscope photo

Sources:

https://ourworldindata.org/monkeypox

https://www.cebm.net/covid-19/excess-mortality-across-countries-in-2020/

https://www.worldometers.info/coronavirus/#countries

googleimages

Some earlier Covid-19 blogs:

https://dodecahedronbooks.blogspot.com/2021/03/covid-19-vaccines-positive-results-from.html

https://dodecahedronbooks.blogspot.com/2021/03/covid-19-vaccines-how-successfully-are.html

https://dodecahedronbooks.blogspot.com/2020/12/covid-19-vaccines-comparison-of.html

https://dodecahedronbooks.blogspot.com/2020/09/covid-19-continues-to-travel-around.html

https://dodecahedronbooks.blogspot.com/2020/07/has-covid-19-become-less-deadly.html

https://dodecahedronbooks.blogspot.com/2020/07/july-2020-update-covid-19-death-rates.html

https://dodecahedronbooks.blogspot.com/2020/05/covid-19-death-rates-correlate-highly.html

https://dodecahedronbooks.blogspot.com/2020/06/covid-19-impact-on-employment-no-impact.html

https://dodecahedronbooks.blogspot.com/2020/04/is-there-model-that-can-predict-when-to.html

https://dodecahedronbooks.blogspot.com/2020/03/estimating-fatality-rate-of-coronavirus.html

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And, here’s a more pleasant travel story than anticipating the worldwide journey of a virus.

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

Spring is on us now, and that brings on thoughts of ROAD TRIP. Sure, it is still a bit early, but you can still start making plans for your next road trip with help of “On the Road with Bronco Billy”. Sit back and go on a ten day trucking trip in a big rig, through western North America, from Alberta to Texas, and back again. Explore the countryside, learn some trucking lingo, and observe the shifting cultural norms across this great continent. Then, come spring, try it out for yourself.

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

Monday 10 October 2022

A Modest Proposal to Fix Twitter

Since Elon Musk (a person for whom I have a lot of respect) is back to buying Twitter, here is my proposal for a really useful Twitter (or any other social media platform on this type).

Conditions for the New Twitter

Only real humans are allowed to sign up.
They are only allowed one account.
The account would have some basic demographic information associated with it, though not much (very general stuff which could not identify people).
It would be free.
They can only post once every 24 hours.
They would have to do the posting personally, no selling or lending of posting rights. No pure “paste and copy”. They would have to make some personal contribution to the post.
They can post on any subject they like. That could span the range (from what they had for dinner to their opinions on international politics, and anything else that they feel to be important.
There would be very little censorship, other than some reasonable standards regarding threats, personal insults, criminal behaviours, etc.
They are only allowed one like every 24 hours.
They are only allowed one retweet every 24 hours.
They are only allowed to comment on one post every 24 hours.
They are only allowed one personal message per 24 hours.
Privacy would be rigorously respected, though aggregate information would be available to any interested researcher, whether affiliated with a larger institution or just working on their own.

I know that enforcing these rules would be difficult, or maybe impossible, but this is a thought experiment or an “ideal-type” case.

Advantages

What are the advantages of this?

It would be a “one person, one vote” expression of public opinion.
No group, political party, religion, movement, etc could artificially inflate their importance.
However, a group could informally canvas their members to post on a particular subject. The fact that members would be leery of “wasting their posts”, would provide a counter-balance to efforts to unduly sway public opinion by any group.
If people wanted to use their daily post to show their fandom of a pop star, political party, cultural product, etc, they could do so. But, in the aggregate, this would reflect the actual feelings of the population.
Similarly for once-per-24 hours likes and retweets.
The limitations would make the entire site more interesting for users, as the content would be refreshed every day with new ideas which would come from varied sources.
One account, which is free and limited to one post per day, would give everyone an equal say.
In other words, this would be authentic “diversity, equity and inclusion.
The limit on posting would ensure that people wouldn’t spend inordinate amounts of time on the site, obsessively posting or getting into pointless comment flame wars. That would help with civility and ensure that people aren’t wasting their precious time, by becoming addicted to the site.
This would also go someway to solving the problem with political polling (selection bias, response bias, etc), as it would be a sort of free-from rolling poll.
Analyzing the data would provide plenty of interesting work for social scientists, which anyone could verify for accuracy, ideological bias, etc (though some might say that providing work for social scientists is of dubious utility).

Problems

What are the potential problems?

Enforcing the rules, obviously. But as I say, this is a thought experiment, the actual implementation details would have to be worked out.
Monetization would be an issue. Perhaps some advertising might be allowed, but the advert to actual post ratio would be maintained at a reasonable level (say one post in ten could be advertising). Since it is “one-post-per-day” there would be competition between advertisers, who would vie for having their post appear on what is equivalent to “prime-time” for the product in question.
Alternatively, it would be a wiki-type venture, where donations would be used to raise the needed revenue.

This would be good for the phone system too. Imagine if telephone solicitors could only make one call per day – oh, what a wonderful world.

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And you should think about going hiking this coming year, to get away from social media for a while.  The Juan de Fuca Marine Trail, on the west coast of Canada is an excellent choice, as you will discover after reading this book (about 100 Kindle normalized pages for only $0.99) :

Amazon U.S. http://www.amazon.com/gp/product/B013VKEXV2

Amazon UK http://www.amazon.co.uk/gp/product/B013VKEXV2

Amazon Canada http://www.amazon.ca/gp/product/B013VKEXV2