Are undiscovered coronaviruses protecting Africa from COVID?

If there is such an undiscovered coronavirus, it will likely be very hard to find. But, scientists from Sierra Leone and the United States may have found its fingerprints. The study focused on characterizing blood samples that were collected from 120 Sierra Leonean patients before SARS-CoV-2 emerged. They compared these blood samples to those of 79 Americans who had not been exposed to SARS-CoV-2.

First they looked at how frequently each population reacted to various coronavirus antigens, that is the parts of the virus that the immune system can recognize. This part of the study focused on the nucleoprotein, which they designated N. Unsurprisingly, both populations appear to have had pretty high exposure to the seasonal coronaviruses. Indeed, roughly half of the American samples positively reacted to nuceloproteins from seasonal coronaviruses hCoV-229E, hCoV-NL53, and hCov-OC43. But even more of the Sierra Leonean samples reacted to these viruses, ranging from just under 70% to about 80%. Maybe this means the known seasonal coronaviruses are more prevalent in Sierra Leone than the US. But, recalling that coronaviruses often cross-react, it is more likely that Sierra Leoneans are just more frequently exposed to coronaviruses in general, including possibly undescribed viruses.

This idea got more support when the two sets of viruses were reacted with nucleoprotein from SARS-CoV-2. Less than five percent of the American samples reacted to SARS-CoV-2 antigen. Since these people are confirmed not to have been exposed to SARS-CoV-2, then this 5% must come from cross-reaction with seasonal coronaviruses that circulate in the US, i.e. the four familiar ones. In comparison, fully 52% of blood samples from Sierra Leoneans collected prior to the Covid-19 pandemic contained antibodies that cross-reacted with SARS-CoV-2.