Inside the Botswana lab that discovered Omicron

Al Jazeera :
The day that Dr Sikhulile Moyo ruefully calls “Omicron Day” started like any normal day, or as normal as one can be for a medical virologist in the middle of a global coronavirus pandemic.
That Friday morning, November 19, the 48-year-old Zimbabwean prayed as usual with his wife and children, wolfed down some cereal and then raced to beat the traffic in Botswana’s capital Gaborone.
On the way to work, the gregarious laboratory director sometimes played his own gospel recordings, but that morning, he listened to a Ghanaian pastor and motivational speaker.
Once at the Botswana Harvard HIV Reference Laboratory (BHHRL), Dr Moyo and his team checked on the PCR tests that lab coordinator Dr Dorcas Maruapula had left running overnight, all taken from Covid-positive samples.
As per their weekly routine, the researchers then processed the nucleic acid – the molecules that make up the virus’s genetic material – extracted from the samples using a palm-sized MinION sequencer. The device produces full sequences of genetic data in real-time that allow the team to look for any evolutionary changes in the virus as it is transmitted. Wonderful Choga, 31, a bioinformatician from Zimbabwe, kept an eye on the computer as the USB-connected MinION outputted genome sequences, his usual cup of coffee at the ready. But later that day, as the team were getting ready to go home, something odd happened.
“There were four sequences showing very strange patterns that we had never seen before. I felt a lot of emotions in my heart,” says Dr Moyo, recalling rising feelings of concern.
On the computer, mismatches in the samples’ genetic code against the original SARS-CoV-2 virus had been flagged across rows of multicoloured letters.
The discrepancies were so great that Dr Moyo worried there was some kind of mistake. But after the team ran thorough quality checks, they still came up with the same results.
“It was quite alarming to us simply because we’d never seen such a lineage in Botswana,” adds Choga. “It was heavily mutated.”