Covid-19: Botswana scientist who sequenced Omicron variant worried by pace of mutation

The pace at which the coronavirus’ Omicron variant accumulated its unusual pattern of mutations is cause for concern, Sikhulile Moyo, the scientist who detected the new strain, said. The speed of the mutations also raises questions over the variant’s evolution and adds to the puzzle of how transmissible it may be.

Botswana Harvard HIV Reference Laboratory Director Moyo said viruses accumulated mutations in multiple steps, Bloomberg reported. He added that it was hard to grasp how early the variant developed given the lack of adequate sequencing of the coronavirus globally.

Scientists are still trying to understand how the Omicron variant mutated so many times in a short space of time, Moyo, who is also a research fellow at Harvard TH Chan School of Public Health, said.

Looking at the previous lineages — the Alpha, the Beta — the mutations accumulated over time, Moyo said.

One theory being floated is that the strain developed in an immuno-compromised person that harboured the virus for a longer-than-normal period. However, Moyo warned that there was no evidence supporting the theory.

Another hypothesis suggests that the virus could have been transferred from a human into an animal host, adapted relatively quickly, and then moved back into humans.

Moyo first sequenced the sample, taken on November 11 from diplomats who had travelled together to Botswana. At that time, the variant most closely resembled the B.1.1.263, known as the UAE lineage and first detected in April 2020.

Looking more closely at the B.1.1.263, he saw that strain had fewer mutations. After seeking additional information from Botswana’s health department about the people from whom the samples were taken, Moyo deposited the findings into an international database on November 23. A few hours later, a group from South Africa reported similar findings. Another group in Hong Kong deposited a partial genome.

With the sheer number of changes in the Omicron variant, Moyo thought it would be a weak virus. Instead, it seemed to be capable of replicating quickly and evading parts of the immune system, causing a higher reinfection risk.

In South Africa, confirmed daily cases have quadrupled from Tuesday as the Omicron variant spreads, showing the new strain’s contagious nature.

Moyo said he was hopeful that as the data poured in, people would go back to their freezers and pull out old samples. Some scientists who have already done that found that the Omicron lineage had been circulating in October.

One big question that scientists are trying to answer is how effective vaccines would be against the variant. The answer could be obtained in weeks, thanks in part to Moyo’s fast response and transparency in sharing his findings.

Moyo told Bloomberg that he was enjoying his contribution to the discovery and how it might have averted several deaths. But it also made him sad to see countries closing their borders and a number of people tweeting and saying scientists had closed Christmas and Moyo believes that’s not how scientists should be rewarded.