Trying to Solve a Covid Mystery: Africa’s Low Death Rates

This is not much of a mystery. Africa has long been plagued by health challenges -- viruses, bacteria and parasites. Most Africans, for instance, are full of worms. You have to be very robusts and have a very good immune system to survive and function there. The less robust have long ago been "weeded out" of the gene pool. So Covid infections are easily resisted

The coronavirus was expected to devastate the continent, but higher-income and better-prepared countries appear to have fared far worse.

KAMAKWIE, Sierra Leone — There are no Covid fears here.
The district’s Covid-19 response center has registered just 11 cases since the start of the pandemic, and no deaths. At the regional hospital, the wards are packed — with malaria patients. The door to the Covid isolation ward is bolted shut and overgrown with weeds. People cram together for weddings, soccer matches, concerts, with no masks in sight.

Sierra Leone, a nation of eight million on the coast of Western Africa, feels like a land inexplicably spared as a plague passed overhead. What has happened — or hasn’t happened — here and in much of sub-Saharan Africa is a great mystery of the pandemic.

The low rate of coronavirus infections, hospitalizations and deaths in West and Central Africa is the focus of a debate that has divided scientists on the continent and beyond. Have the sick or dead simply not been counted? If Covid has in fact done less damage here, why is that? If it has been just as vicious, how have we missed it?

The first iteration of the virus that raced around the world had comparatively minimal impact here. The Beta variant ravaged South Africa, as did Delta and Omicron, yet much of the rest of the continent did not record similar death tolls.

Into Year Three of the pandemic, new research shows there is no longer any question of whether Covid has spread widely in Africa. It has.

Studies that tested blood samples for antibodies to SARS-CoV-2, the official name for the virus that causes Covid, show that about two-thirds of the population in most sub-Saharan countries do indeed have those antibodies. Since only 14 percent of the population has received any kind of Covid vaccination, the antibodies are overwhelmingly from infection.

A new W.H.O.-led analysis, not yet peer-reviewed, synthesized surveys from across the continent and found that 65 percent of Africans had been infected by the third quarter of 2021, higher than the rate in many parts of the world. Just 4 percent of Africans had been vaccinated when these data were gathered.

So the virus is in Africa. Is it killing fewer people?
Some speculation has focused on the relative youth of Africans. Their median age is 19 years, compared with 43 in Europe and 38 in the United States. Nearly two-thirds of the population in sub-Saharan Africa is under 25, and only 3 percent is 65 or older. That means far fewer people, comparatively, have lived long enough to develop the health issues (cardiovascular disease, diabetes, chronic respiratory disease and cancer) that can sharply increase the risk of severe disease and death from Covid. Young people infected by the coronavirus are often asymptomatic, which could account for the low number of reported cases.

Plenty of other hypotheses have been floated. High temperatures and the fact that much of life is spent outdoors could be preventing spread. Or the low population density in many areas, or limited public transportation infrastructure. Perhaps exposure to other pathogens, including coronaviruses and deadly infections such as Lassa fever and Ebola, has somehow offered protection.

Since Covid tore through South and Southeast Asia last year, it has become harder to accept these theories. After all, the population of India is young, too (with a median age of 28), and temperatures in the country are also relatively high. But researchers have found that the Delta variant caused millions of deaths in India, far more than the 400,000 officially reported. And rates of infection with malaria and other coronaviruses are high in places, including India, that have also seen high Covid fatality rates.

So are Covid deaths in Africa simply not counted?

Most global Covid trackers register no cases in Sierra Leone because testing for the virus here is effectively nonexistent. With no testing, there are no cases to report. A research project at Njala University in Sierra Leone has found that 78 percent of people have antibodies for this coronavirus. Yet Sierra Leone has reported only 125 Covid deaths since the start of the pandemic.

Most people die in their homes, not in hospitals, either because they can’t reach a medical facility or because their families take them home to die. Many deaths are never registered with civil authorities.

This pattern is common across sub-Saharan Africa. A recent survey by the United Nations Economic Commission for Africa found that official registration systems captured only one in three deaths.

But many scientists tracking the pandemic on the ground disagree. It’s not possible that hundreds of thousands or even millions of Covid deaths could have gone unnoticed, they say.
“We have not seen massive burials in Africa. If that had happened, we’d have seen it,” said Dr. Thierno Baldé, who runs the W.H.O.’s Covid emergency response in Africa.

“A death in Africa never goes unrecorded, as much as we are poor at record-keeping,” said Dr. Abdhalah Ziraba, an epidemiologist at the African Population and Health Research Center in Nairobi, Kenya. “There is a funeral, an announcement: A burial is never done within a week because it is a big event. For someone sitting in New York hypothesizing that they were unrecorded — well, we may not have the accurate numbers, but the perception is palpable. In the media, in your social circle, you know if there are deaths.”

Dr. Demby, the Sierra Leone health minister, who is an epidemiologist by training, agreed. “We haven’t had overflowing hospitals. We haven’t,” he said. “There is no evidence that excess deaths are occurring.”

https://archive.ph/HTzhV

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Scientists identify antibodies that can neutralize omicron

An international team of scientists have identified antibodies that neutralize omicron and other SARS-CoV-2 variants. These antibodies target areas of the virus spike protein that remain essentially unchanged as the viruses mutate.

By identifying the targets of these "broadly neutralizing" antibodies on the spike protein, it might be possible to design vaccines and antibody treatments that will be effective against not only the omicron variant but other variants that may emerge in the future, said David Veesler, investigator with the Howard Hughes Medical Institute and associate professor of biochemistry at the University of Washington School of Medicine in Seattle. "This finding tells us that by focusing on antibodies that target these highly conserved sites on the spike protein, there is a way to overcome the virus' continual evolution," Veesler said.

Veesler led the research project with Davide Corti of Humabs Biomed SA, Vir Biotechnology, in Switzerland. The study's findings were published Dec. 23 in the journal Nature. The lead authors of the study were Elisabetta Cameroni and Christian Saliba (Humabs), John E. Bowen (UW Biochesmistry) and Laura Rosen (Vir).

The omicron variant has 37 mutations in the spike protein, which it uses to latch onto and invade cells. This is an unusually high number of mutations. It is thought that these changes explain in part why the variant has been able to spread so rapidly, to infect people who have been vaccinated and to reinfect those who have previously been infected.

"The main questions we were trying to answer were: how has this constellation of mutations in the spike protein of the omicron variant affected its ability to bind to cells and to evade the immune system's antibody responses," Veesler said.

[Veesler and his colleagues speculate that omicron's large number of mutations might have accumulated during a prolonged infection in someone with a weakened immune system or by the virus jumping from humans to an animal species and back again.]

To assess the effect of these mutations, the researchers engineered a disabled, nonreplicating virus, called a pseudovirus, to produce spike proteins on its surface, as coronaviruses do. They then created pseudoviruses that had spike proteins with the omicron mutations and those found on the earliest variants identified in the pandemic.

The researchers first looked to see how well the different versions of the spike protein were able to bind to protein on the surface of cells, that the virus uses to latch onto and enter the cell. This protein is called the angiotensin converting enzyme-2 (ACE2) receptor.

They found the omicron variant spike protein was able to bind 2.4 times better than spike protein found in the virus isolated at the very beginning of the pandemic. "That's not a huge increase," Veesler noted, "but in the SARS outbreak in 2002-2003, mutations in the spike protein that increased affinity were associated with higher transmissibility and infectivity." They also found that the omicron version was able to bind to mouse ACE2 receptors efficiently, suggesting omicron might be able to "ping-pong" between humans and other mammals.

The researchers then looked at how well antibodies against earlier isolates of the virus protected against the omicron variant. They did this by using antibodies from patients who had previously been infected with earlier versions of the virus, vaccinated against earlier strains of the virus, or had been infected and then vaccinated.

They found that antibodies from people who had been infected by earlier strains and from those who had received one of the six most-used vaccines currently available all had reduced ability to block infection.

Antibodies from people who had previously been infected and those who had received the Sputnik V or Sinopharm vaccines as well as a single dose of Johnson & Johnson had little or no ability to block—or "neutralize"—the omicron variant's entry into cells. Antibodies from people who had received two doses of the Moderna, Pfizer/BioNTech, and AstraZeneca vaccines retained some neutralizing activity, albeit reduced by 20- to 40-fold, much more than any other variants.

Antibodies from people who had been infected, recovered, and then had two doses of vaccine also had reduced activity, but the reduction was less, about fivefold, clearly demonstrating that vaccination after infection is useful.

Antibodies from people, in this case a group of renal dialysis patients, who had received a booster with a third dose of the mRNA vaccines produced by Moderna and Pfizer/BioNTech showed only a 4-fold reduction in neutralizing activity. "This shows that a third dose is really, really helpful against omicron," Veesler said.

All but one antibody treatments currently authorized or approved to be used with patients exposed to the virus, had no or had markedly reduced activity against omicron in the laboratory. The exception was an antibody called sotrovimab, which had a two- to three-fold reduction of neutralizing activity, the study finds.

But when they tested a larger panel of antibodies that have been generated against earlier versions of the virus, the researchers identified four classes of antibodies that retained their ability to neutralize omicron. Members of each of these classes target one of four specific areas of the spike protein present in not only SARS-CoV-2 variants but also a group of related coronaviruses, called sarbecoviruses. These sites on the protein may persist because they play an essential function that the protein would lose if they mutated. Such areas are called "conserved."

The finding that antibodies are able to neutralize via recognition of conserved areas in so many different variants of the virus suggests that designing vaccines and antibody treatments that target these regions could be effective against a broad spectrum of variants that emerge through mutation, Veesler said.

https://medicalxpress.com/news/2021-12-scientists-antibodies-neutralize-omicron.html

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Also see my other blogs. Main ones below:

http://edwatch.blogspot.com (EDUCATION WATCH)

http://antigreen.blogspot.com (GREENIE WATCH)

http://pcwatch.blogspot.com (POLITICAL CORRECTNESS WATCH)

http://australian-politics.blogspot.com/ (AUSTRALIAN POLITICS)

http://snorphty.blogspot.com/ (TONGUE-TIED)

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