Scientists are struggling to explain observations that the morbility and mortality rates in SARS-CoV-2 antibody positive people in sub-Saharan African is remarkably low. Neither has there been a significant growth in the death rate. Even stranger, this does not seem to be the case in South Africa where cases have followed a similar pattern to Europe and North America.
Although Africa reported its millionth official COVID-19 case last week, it seems to have weathered the pandemic relatively well so far, with fewer than one confirmed case for every thousand people and just 23,000 deaths so far. Yet several antibody surveys suggest far more Africans have been infected with the coronavirus—a discrepancy that is puzzling scientists around the continent. “We do not have an answer,” says immunologist Sophie Uyoga at the Kenya Medical Research Institute–Wellcome Trust Research Programme.
After testing more than 3000 blood donors, Uyoga and colleagues estimated in a preprint last month that one in 20 Kenyans aged 15 to 64—or 1.6 million people—has antibodies to SARS-CoV-2, an indication of past infection. That would put Kenya on a par with Spain in mid-May when that country was descending from its coronavirus peak and (Spain) had 27,000 official COVID-19 deaths. Kenya’s official toll stood at 100 when the study ended. And Kenya’s hospitals are not reporting huge numbers of people with COVID-19 symptoms.
Other antibody studies in Africa have yielded similarly surprising findings. From a survey of 500 asymptomatic health care workers in Blantyre, Malawi, immunologist Kondwani Jambo of the Malawi–Liverpool Wellcome Trust Clinical Research Programme and colleagues concluded that up to 12.3% of them had been exposed to the coronavirus. Based on those findings and mortality ratios for COVID-19 elsewhere, they estimated that the reported number of deaths in Blantyre at the time, 17, was eight times lower than expected.
It should be noted that these studies are in pre-print and have not been peer-review published. They have however been conducted by highly reputable institutions. As might be expected from the demographics in Africa, the median age of cases (18 and 20) is much lower than in Europe where it is in the 40s however the number of serious cases and deaths are still much lower when age adjustments are made. Dr John Campbell has covered this apparent immunity or resistance to COVID-19 in one of his informative videos.
So if the effect is real, as it appears to be, what is causing it? Why does the Sahara desert form some sort of cordon sanitaire, not to the spread of the virus but to much lessen its affect on the population. Why is the affect not shown in South Africa particularly when neighboring Mozambique is following the “sub-Sahara” pattern?
One possibility being investigated is immunity brought on by other infections. Malaria looks like a possible candidate but Africans have the same human coronaviruses like cold and flu as elsewhere and John Campbell does not think this is the cause. It did however raise a lot of discussion among the community who watch Cambell’s videos which include a lot of medical professionals. he followed up with a report on the suggestions that had been made.
One factor may be the huge genetic diversity among sub-Saharan Africans. Another genetic factor may be that, despite this diversity, they do not share Neanderthal DNA. In other populations, this DNA appears to have some associations with immune response. This might explain South Africa where the native tribes migrated fairly late so might not have developed further genetic diversity. There are some facial stereotypes associated with the different tribes even now.
Another might be follow from another observation. Some people appear to have partial immunity to SARS-CoV-2 but the antibodies they already have do not attack the same “spike” part of the virus that is being targetted by the vaccines being developed. Speculation is that they have previously been infected with animal beta-coronaviruses. These are found in bats, dogs, rodents and cattle. Dr Campbell has not gone into this in length but it does seem a strong possibility to me. It would be like cowpox protecting from smallpox.
Let’s speculate. Assume there a particular animal beta-coronavirus or a combination unique to sub-Saharan Africa, exposure to which provides a degree of protection at least from the worst effects of COVID-19? Could the virus be unique to acertain animal only found in that region but which is in contact with people enough to make asymptomatic infection widespread?
Well there is at least one candidate:
Predominantly nocturnal, giant pouched rats are omnivorous and are found throughout sub-Saharan Africa, except for southern South Africa. Habitats in which they live include forests and woodlands, as well as gardens, orchards (where they climb fruit trees during the day), and sometimes houses.
Two species are hunted for food. They may not have to be in immediate contact with humans to transmit harmless beta-coronaviruses to them. We know, for example, that SARS-CoV-2 can be shed in body waste. Food can easily be contaminated either in the farm or storage. In most of Africa, farmers literally take their produce and animals to the market. Even in the big cities food is typically bought in open markets and even in shops storage is not as scrupulous as in Wal-Mart for example. Food is often home grown to provide supplements to the widespread staple mealy meal (like US grits).
Geographic spread of pouched rats may go towards explaining some of South Africa’s worse COVID-19 record but there is another significant factor. South Africa is much more like North America, with the exception of free government health-care. Over the course of the last two centuries, its mineral and agricultural recourses have been exploited on an industrial scale. It has huge fruit and wine exports and of course gold and diamonds. During Apartheid, an oil embargo meant some of the country’s coal resources were used to make gasoline. The suburbs of Johannesburg have shopping malls. The crime situation has meant that there is a trend the well-off are moving from their homes in large open lots to gated communities.
I am not ignoring the areas of South Africa that are less productive which were assigned as “homelands” under Apartheid. (A bit like the native American tribes being assigned reservations). There are certainly areas where life is much more like rural life elsewhere Africa. Some though like Bophuthatswa were quite developed through income from minerals and gambling. The Sun City casino complex is convenient for Joburg and Pretoria. Under Apartheid gambling was prohibited but the “homelands” were considered by the regime to be independent countries. A bit like Indian reservations they could make their own gaming laws.
To serve the large urban populations working in the mines, factories and offices and the farm workers on those vinyards and fruit farms, a much more Western growing and distribution system has developed. The rats are at the southern edge of their range. They are unlikely to raid monocultures and would be suppressed if they did. Farm produce is often harvested mechanically. It is often washed and packed before being dispatched to markets, It’s stored in better warehouses and sold in more hygenic conditions. In short, the food supply system and the demographics mean that South Africans are much less likely to be infected by the rat beta-coronavirus. The population has not built up herd immunity to it which provides partial immunity to SARS-CoV-19.
Now this is me surmising but it is the sort of thought process that researchers will be going through when trying to find the link. If it is shown by latter testing and outcomes to be a real phenomenon, the lower morbidity and mortality rate in sub-Saharan Africans is really good news.
