Two new omicron sublineages discovered by South African scientists

South African scientists have discovered two new sublineages of the omicron coronavirus variant, said Tulio de Oliveira, who runs gene-sequencing institutions in the country.

The lineages have been named BA.4 and BA.5, he said by text message and in a series of tweets. Still, de Oliveira said, the lineages have not caused a spike in infections in South Africa and have been found in samples from a number of countries.

“Given the very low infections, hospitalizations and deaths in South Africa we are alerted about the continued evolution but not concerned,” de Oliveira, said by text message. “All of the laboratory science on virus neutralization and vaccines are already under way and we are strengthening genomic surveillance.”

South Africa and Botswana were the first to discover omicron in November and South Africa was the first country to be hit by a wave of infections caused by the strain. Hospitalizations and deaths were a fraction of those caused by the delta variant even as daily cases hit a record in December.

The sublineages have also been found in samples from Botswana, Belgium, Germany, Denmark and the U.K., de Oliveira said on Twitter.

The two lineages have similar mutations on their spike proteins, the part of the virus that helps the virus attach to human cells, to the BA.2 sublineage which appears to be more infectious than the original omicron strain. They also have some additional mutations, he said.

The two sublineages differ from each other in terms of amino acid mutations outside the spike protein, he said. Botswana has also announced the discovery of the variants.

South Africa on Monday reported 553 new coronavirus cases with 5% of tests coming back positive.