Q: The South Africa variant of the coronavirus was first identified in South Carolina, and the two patients reportedly had no travel history and no known ties to each other. Does this mean the mutation started in South Africa and there was community spread that was not previously detected, or is it a natural, even expected, mutation that just happened to be identified in South Africa before it was identified in the U.S.?
A: Information about the different variants is rapidly emerging. There are a few things that we do know for sure, but there are still gaps in our knowledge. For one, as you note, we do know that viruses mutate often over time.
The coronavirus has actually been mutating since it was originally identified, but genetic changes have been small and not significant. The most recent variants, however, seem to have more of an impact on how easily the virus can spread. Labs in the U.S. and across the world have generated thousands of coronavirus genetic sequences that have contributed to our understanding of how the virus mutates.
The Centers for Disease Control and Prevention acknowledges, however, that there are considerable gaps in the U.S. representation of surveillance data for coronavirus sequencing, which may explain why this variant was identified elsewhere first. It is possible, then, that the South African variant, like those identified from the United Kingdom and Brazil, was already in the U.S., and just went unchecked.
The CDC is boosting surveillance efforts to collaborate with labs around the country, which will help in identifying variants sooner. Early recognition helps scientists understand the virus’ unique characteristics and will help in understanding how it spreads, whether vaccines will be protective and how they may affect viral testing.