Where Did The Coronavirus Variants Come From?

Scientists are looking at a possible link between the mutations in the U.K. and South Africa — and those in immunocompromised patients who are infected with COVID-19.

Transcript

AUDIE CORNISH, HOST:

For weeks, there's been a lot of worry about the changing coronavirus. COVID has been mutating into variants that are more transmissible, less responsive to vaccines and make reinfections more common. Three of these variants have now spread all over the world, including to the U.S. Scientists say the coronavirus has mutated surprisingly fast. NPR's Michaeleen Doucleff tells us why they think that's happening.

MICHAELEEN DOUCLEFF, BYLINE: Back in the spring last year, a 45-year-old man came to the Brigham and Women's Hospital in Boston with COVID-19. Dr. Jonathan Li helped to treat him, and he got better, so doctors discharged him. But his infection never went away.

JONATHAN LI: This is an extraordinary individual who was readmitted over the subsequent five months several times for recurrence of his COVID infection and severe pneumonia.

DOUCLEFF: Just to be clear here, Li is not talking about what is referred to as long-haulers - people who get COVID, clear their infection but continue to have some problems. This man, Li says, had living, growing virus in his body for 154 days, which was extremely unusual. He had never seen it before.

LI: That is one of the remarkable aspects of this case. And, in fact, he was highly infectious even five months after the initial diagnosis.

DOUCLEFF: Li says the man's immune system wasn't working normally. He was taking immunosuppressive drugs for a chronic illness, so his body couldn't fight off the virus very well. But Li also wondered if perhaps the virus was taking advantage of this unusual situation. With so much time inside the man, the virus might have the opportunity to test out different versions of itself and find more infectious versions. So Li and his colleagues began to examine the virus' genes. Li couldn't believe what they found.

LI: I was shocked.

DOUCLEFF: Shocked because the virus was mutating very quickly inside the man's body. These mutations allowed it to evade his immune system to escape detection by antibodies.

LI: When I saw the virus and the viral sequence, I think I knew then that this - that we were dealing with something completely different and potentially very important.

DOUCLEFF: Completely different because the virus had a whole collection of mutations, not just one or two but more than 20. Scientists had never seen this before during the whole pandemic. Li and his team published the findings in the New England Journal of Medicine. The report didn't even make big news. That was November 2020. Then about a month later...

(SOUNDBITE OF ARCHIVED NPR BROADCAST)

DAVID GREENE: A new coronavirus variant is spreading rapidly in London and other parts of southeast England, and it is causing international concern.

DOUCLEFF: As NPR's David Greene reported, scientists this past December detected new genetic variants of the virus - one in the U.K., one in South Africa and then, later, one in Brazil. Guess what these variants have in common with the virus in the Boston patient?

JEREMY LUBAN: A sudden collection of multiple mutations in a combination that is worrisome.

DOUCLEFF: That's Jeremy Luban. He's a virologist at the University of Massachusetts Medical School. He says these new variants look remarkably similar to the virus Li and his colleagues found in their patient. They aren't the same, but they share important characteristics. They both have about 20 mutations, and they have ones that make the virus more contagious. And so right now, Luban says, one hypothesis is that the new variants - the one from the U.K., South Africa and Brazil - arose inside people like the Boston patient, people with these long-term infections and who are immunocompromised.

LUBAN: Because their immune system was not working normally, they could not eliminate the virus. And over time, the virus then acquired a collection of mutations that otherwise had not been seen before.

DOUCLEFF: In other words, the virus used this long-term infection as a testing ground to try out different mutations and see which ones evade the immune system, become more infectious and, eventually, spread more easily around the world. Michaeleen Doucleff, NPR News. Transcript provided by NPR, Copyright NPR.