How a Harvard-affiliated lab in Botswana became the first to identify the Omicron variant

The main building of the Harvard-Botswana partnership is in Gaborone Botswana.Botswana Harvard Aids Institute Partnership
The main building of the Harvard-Botswana partnership is in Gaborone Botswana.Botswana Harvard Aids Institute Partnership

As the rows of multi-coloured letters lit up his computer screen at the Botswana-Harvard AIDS Institute Partnership, Sikhulile Moyo looked on in surprise. The letters represented the genetic codes from thousands of coronavirus samples.

But one line stuck out: It looked like a swath of multiple mutations. It was Friday, November 19. Moyo’s lab in Gaborone, Botswana, a city just over the northern border of South Africa, had been sequencing the genomes of about 95 coronavirus samples every week to track mutations, the natural changes that occur in virus genes. But he’d never seen anything like this before. While other Harvard affiliates, including the Broad Institute and the major Boston hospitals, have seized the limelight in coping with COVID-19, this little-known African outpost would end up playing a critical role as the first lab to identify the new variant that has transfixed the world. “This sequence really shocked us,” Moyo, the laboratory director, said in an interview Monday. He showed it to a colleague, who agreed it looked like nothing seen before in Botswana.

Could it have come from somewhere else? The Delta variant hit the US economy hard. Will Omicron pack a similar punch? Over the next few days, comparing the findings with international databases of coronavirus genomes from around the world, Moyo’s team confirmed that the mutations, found in four samples, had not been seen anywhere else in the world. And there were a lot of them, about 50. “When you see a constellation of mutations you begin to wonder what kind of virus this is and what kind of impact it might have,” he said. On November 23, Moyo’s team deposited their findings into an open international database, available to scientists worldwide.

Editor's Comment
Bravo, Matlala JSS for recognising employees!

Last Friday, Matlala Junior Secondary School (JSS) in Tlokweng did just that – they organised an event to honour their teachers and support staff. This gesture is truly commendable, as teachers occupy a pivotal role in the lives of our children.To be completely candid, teachers are the ones who shape our children from a very tender age, investing a significant amount of time in their growth and development. It's not uncommon to hear parents...

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