Africa is a mystery - Printable Version
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Africa is a mystery - OutsiderFan - 08-14-2020
I just watched video this morning from Dr. John Campbell on Youtube that presented pretty head scratching data out of Africa.
The gist is many of the more poor countries in Africa are showing high rated of SARS-CoV-2 in the population, but hardly anyone is getting really sick or dying. What makes it even more bizarre is South Africa is struggling with it on par with Europe, the Americas, and India.
The assumption was poor African countries with poor health systems would be ravaged by the pandemic, but it simply has not happened. Some theories:
- High exposure to other coronaviruses has created cross-immunity
- Exposure to Malaria and Dengue Fever might have created cross-immunity
- Lower median ages for most African countries
- High Vitamin D exposure
But none of these really seem to adequately answer the question as to why poor sub-Saharan countries in Africa are avoiding the scale of complications and death that more developed countries on other continents have. Again, testing has revealed high seroprevalence in the population, just not much damage coming from the infections.
Any of y'all have any ideas?
RE: Africa is a mystery - M T - 08-14-2020
The 4 theories for better outcome have been around since the early days of COVID-19, except that "Exposure to malaria, ..." is usually phrased as having had the medications or vaccines for them.
The lower median age can be accounted for with demographics. Just look at the disease outcomes in specific age groups. I'd also throw in the possibility that there may be fewer percentage people in older age groups with the comorbidities (as they died already). I DO NOT KNOW THAT IS TRUE.
My naive expectation is that the African population gets far more vitamin D than the "Western Civilization". While there was suggestive evidence of its benefit, I haven't seen studies confirming or refuting it.
RE: Africa is a mystery - BostonCard - 08-14-2020
I'm sorry, I'm not seeing a paradox here. There have been 1,089,894 cases and 24,752 deaths in Africa as a whole. Thus naive CFR (deaths reported/cases reported) in Africa as a whole is 2.3%. In South Africa, which accounts for over half of the cases, you have 11,270 deaths and 572,865 reported cases, and a CFR of 2.0%. Thus outside of South Africa, the CFR is 2.6%. I'm guessing that a lot of the cases and a lot of the deaths are simply not being counted. Many don't even come in contact with the healthcare system, and die at home.
I compared that to some other poor to middle income countries. In South Asia, the CFR in India is 2.0%; in Pakistan it is 2.1%, in Bangladesh it is 1.3% and in Afghanistan it is 3.6%. In Southeast Asia, it is 1.7% in Indonesia and 1.6% in the Philippines. In South America, it is 2% in Argentina an 0.9% in Venezuela.
The numbers are higher in "hard hit" areas that have been overwhelmed. I think in those areas, like Spain, Italy, and the Northeast US, the observed CFR is much higher mostly because non-seriously ill patients were not tested. For example, the the CFR overall in the US is 3.1%; however outside of New York and New Jersey, the crude CFR is 2.5%.
So much of the numbers are dependent on who gets tested that looking at crude CFR is pretty meaningless. It would be most interesting to look at an estimate of IFR derived by comparing the total number of excess deaths by estimates of infected based on serology. In Spain, where that was best done the infection fatality rate for Spain as a whole was 1.15% and varied between 0.13% and 3.25% in the regions (https://www.mdpi.com/2079-7737/9/6/128/pdf), compared to a crude CFR of 8.0%.
In other words, using CFR is kind of pointless, because the biggest variable is how well the testing has been carried out.
BC
RE: Africa is a mystery - CardinalSagehen - 08-14-2020
I don't know if this applies to most of Africa, and it's just a theory that might have been shared here previously, but I found the following study to be interesting. It suggests that countries with high vaccination rates for tuberculosis, such as Germany, have done much better in terms of COVID-19 mortality. The theory is that there may be some cross-immunity. Almost all countries in Africa have a current policy to vaccinate for TB, although I don't know how successful those policies are. Places like the US, where TB has not been endemic, have never had a TB vaccination policy.
https://www.pnas.org/content/117/30/17720.full
Quote:A strong correlation between the BCG index, an estimation of the degree of universal BCG vaccination deployment in a country, and COVID-19 mortality in different socially similar European countries was observed (r2 = 0.88; P = 8 × 10−7), indicating that every 10% increase in the BCG index was associated with a 10.4% reduction in COVID-19 mortality. Results fail to confirm the null hypothesis of no association between BCG vaccination and COVID-19 mortality, and suggest that BCG could have a protective effect. Nevertheless, the analyses are restricted to coarse-scale signals and should be considered with caution.
![[Image: F1.large.jpg]](https://www.pnas.org/content/pnas/117/30/17720/F1.large.jpg)
RE: Africa is a mystery - BostonCard - 08-14-2020
I'm old enough to remember when a correlation was found between latitude and COVID-19 and everyone thought that it was because of temperature and that it suggested that COVID-19 was going to go away in the summer.
I remember when early in the pandemic people were wondering why Germany's CFR was so low; it has since caught up with much of the rest of the world (excepting countries that were overwhelmed).
I think most of these ecological correlations are likely to turn out spurious. Numbers of cases and even deaths attributed to COVID-19 are very subject to the testing regimen, which has been very uneven. In some countries *cough, Russia, cough*, the numbers are manipulated to fit the country's narrative. Even deaths, which I thought would be harder to get wrong, are frequently under-counted (see, for example, this article: https://www.nytimes.com/interactive/2020/08/12/us/covid-deaths-us.html).
I would not trust any analysis that depended on reported COVID-19 cases and deaths.
BC
RE: Africa is a mystery - CardinalSagehen - 08-14-2020
(08-14-2020, 09:43 AM)BostonCard Wrote: I'm old enough to remember when a correlation was found between latitude and COVID-19 and everyone thought that it was because of temperature and that it suggested that COVID-19 was going to go away in the summer.
I remember when early in the pandemic people were wondering why Germany's CFR was so low; it has since caught up with much of the rest of the world (excepting countries that were overwhelmed).
I think most of these ecological correlations are likely to turn out spurious. Numbers of cases and even deaths attributed to COVID-19 are very subject to the testing regimen, which has been very uneven. In some countries *cough, Russia, cough*, the numbers are manipulated to fit the country's narrative. Even deaths, which I thought would be harder to get wrong, are frequently under-counted (see, for example, this article: https://www.nytimes.com/interactive/2020/08/12/us/covid-deaths-us.html).
I would not trust any analysis that depended on reported COVID-19 cases and deaths.
BC
I agree with that. Case stats are meaningless, so CFRs are meaningless. This one seems to be based on death rates in European counties, which I assume to be a fairly reliable stat. But the correlation will likely prove to be random.
It's pretty much impossible to know what is really going on in Africa.
RE: Africa is a mystery - OutsiderFan - 08-14-2020
Check out the notes in the Youtube video below for the source data:
https://www.youtube.com/watch?v=bQcS-UWBq4Q
RE: Africa is a mystery - BostonCard - 08-14-2020
https://www.economist.com/graphic-detail/2020/07/15/tracking-covid-19-excess-deaths-across-countries
Take a look at the excess deaths for South Africa, on the bottom row of graphs (the only country that has a good enough weekly mortality reporting that you can reliably calculate excess deaths) and compare it to the COVID-19 attributed deaths. A lot of deaths due to COVID-19 are simply not being captured in South Africa, and I suspect continent-wide.
This is a case where Occam's razor applies. When unreliable data seems to show something that doesn't make sense, the most likely reason is that the data is unreliable.
BC
RE: Africa is a mystery - ATLcardinal - 08-14-2020
Things have gotten better in South Africa since Mbeki notoriously manipulated the death certificates and claimed no HIV problem when in fact HIV was the leading cause of death in South Africa. But... virus information from Africa should be consided suspect unless proven otherwise and as BC has explained the published rates are all wrong because of lack of testing. I don't think Campbell in the video understands how the numbers work, at least in the first Kenya example which was as far as I watched. He mixes up a serology survey implying 5% infection rate in the country with a published number of COVID-19 deaths at the time of 71, which leads to an incredibly low fatality rate. However in most countries (and states) the COVID-19 death figures require a confirmed COVID-19 diagnosis which requires a positive COVID-19 test. If no COVID-19 test, no COVID-19 death, and if 5% really were infected virtually none of the deaths in that group are being counted because the positive tested numbers in Kenya are a tiny fraction of that.
Campbell is a retired nurse/teacher and seems like a motivated and well-meaning guy but may not have the statistics and epidemiology background for the conclusions he is reaching.
RE: Africa is a mystery - OutsiderFan - 08-14-2020
To be fair to Campbell, he's not saying he knows what is happening. Just presenting data trying to be optimistic about what it means, and asking questions trying to understand what is going on, like many of us.
RE: Africa is a mystery - BostonCard - 08-14-2020
Also, to be fair to him, he cites the following (news) article in Science, which makes the same mistake about serology data and mortality data:
https://www.sciencemag.org/news/2020/08/pandemic-appears-have-spared-africa-so-far-scientists-are-struggling-explain-why
Quote:Scientists who surveyed about 10,000 people in the northeastern cities of Nampula and Pemba in Mozambique found antibodies to SARS-CoV-2 in 3% to 10% of participants, depending on their occupation; market vendors had the highest rates, followed by health workers. Yet in Nampula, a city of approximately 750,000, a mere 300 infections had been confirmed at the time. Mozambique only has 16 confirmed COVID-19 deaths. Yap Boum, a microbiologist and epidemiologist with Epicentre Africa, the research and training arm of Doctors Without Borders, says he found a high prevalence of SARS-CoV-2 antibodies in people from Cameroon as well, a result that remains unpublished.
So what explains the brobdingnagian gap between antibody data on the one hand and the official case and death counts on the other? Part of the reason may be that Africa misses many more cases than other parts of the world because it has far less testing capacity. Kenya tests about one in every 10,000 inhabitants daily for active SARS-CoV-2 infections, one-tenth of the rate in Spain or Canada. Nigeria, the continent’s most populous nation, tests one out of every 50,000 people per day. Even many people who die from COVID-19 may not get a proper diagnosis.
But in that case, you would still expect an overall rise in mortality, which Kenya has not seen, says pathologist Anne Barasa of the University of Nairobi who did not participate in the country’s coronavirus antibody study. (In South Africa, by contrast, the number of excess natural deaths reported between 6 May and 28 July exceeded its official COVID-19 death toll by a factor of four to one.) Uyoga cautions that the pandemic has hamstrung Kenya’s mortality surveillance system, however, as fieldworkers have been unable to move around.
But again, that caveat ("the pandemic has hamstrung Kenya’s mortality surveillance system, however, as fieldworkers have been unable to move around.") is pretty important.
By the way, I didn't mean to be harsh on ecological analyses earlier. Correlations from ecological analyses are very important to generate hypotheses. Many (in my experience) most have innocent explanations and don't pan out, but every once in a while an important insight will come from a hypothesis that arose from an ecological correlation. That being said, a skeptical eye is warranted, especially before invoking "just so stories" as explanations.
BC
RE: Africa is a mystery - akiddoc - 08-15-2020
African countries generally do not have well developed public health departments. There isn't much testing. I can't imagine the statistics are dependable.
Other things to consider: Life expectancy in Africa is MUCH lower than it is here. For example, in Nigeria it is about 54 yo. There just aren't that many people over the age of 70, which is the age group with very high mortality. Another issue is that autoimmune disease is much less common in most of Africa than it is in North America and Europe. Different diets and more frequent parasitic infections are thought to be contributory. Since it is the inflammatory response that kills you most of the time with Covid 19, this could explain the low death rate. I doubt there is a different resistance to infection, but there is likely a different outcome from infection.
RE: Africa is a mystery - OutsiderFan - 08-17-2020
If it is true that Covid-19 is less harmful to African populations because some sort of biological defenses have been developed in people exposed to myriad pathogens, while others who have lived a more "sheltered" infection life suffer in greater numbers, it certainly raises some existential and philosophical questions about medical and scientific ethics, as well as the perils of Humans as apex predators with nothing to thin the herd.
We have this idea that we protect ourselves with better medicine and avoiding disease. But maybe we have become too weak and vulnerable as a species by not having to face the gauntlet of disease those in Africa have. Maybe a little less "save everyone" and a little more "let nature take its course" is warranted? It doesn't seem the ideal trajectory for life on Earth is pushing 8 Billion Humans on it.
RE: Africa is a mystery - BostonCard - 08-17-2020
Acute respiratory infections (ARI), particularly lower respiratory tract infections (LRTI; basically influenza and pneumonia), are the leading cause of death among children under five years of age and are estimated to be responsible for between 1.9 million and 2.2 million childhood deaths globally each year. Forty-two percent of these ARI-associated deaths occur in Africa.
TB kills 1.7 million people each year, 417,000 of its victims were in Africa.
Malaria kills about 400,000 people each year, 94% of whom are in Africa.
The burden of yellow fever in Africa is estimated at 84,000–170,000 severe cases and 29,000–60,000 deaths each year.
Cholera kills 7000 people in Africa each year.
and on and on
But yeah, let's accept the burden of these illnesses so that we are less vulnerable to COVID-19, which has killed 775,000 people worldwide. The idea that we ought to "let nature take its course" is one of the most asinine suggestions I've seen on this board.
BC
RE: Africa is a mystery - akiddoc - 08-17-2020
To expand upon BC's comment, the price we pay for longer more comfortable lives is a different set of diseases that might eventually kill us. That's okay as far as I'm concerned.
With respect to autoimmune and inflammatory diseases generally, we could reduce the incidence in the population by eating properly and exercising. That could be said for virtually every disease, though.
Leftcoast - Leftcoast - 08-17-2020
Before WWI Europe had seen 40 years of relative peace and some bemoaned the younger generation as weak since they hadn’t been ennobled and disciplined by the experience of war.
Along came the rest of the 20th century and Europe no longer romanticizes war.
I’ll file “Let nature take its course” with those pre-WWI complaints. We don’t want whatever sort of “strength” a lack of modern medicine might bring.