Covid-19: Omicron mutations may provide clues to its origin

RIO DE JANEIRO, BRAZIL – Omicron’s exceptionally large number of mutations on the gene that helps the coronavirus spread may provide clues as to how it developed, according to a computer analysis of the variant.

The coexistence of mutations in the so-called S gene, which would normally inhibit the virus’ ability to thrive, suggests that the changes are instead working to help the variant become more effective at spreading, according to a blog post by researchers led by Associate Professor Darren Martin of the Institute of Infectious Diseases and Molecular Medicine at the University of Cape Town.

“While individually mutations can decrease the fitness of any genome in which they occur, collectively they can compensate for each other’s deficits to produce a more suitable virus genotype,” the researchers wrote.

Scientists have been rushing to answer questions about the Omicron, which was first sequenced in Botswana and South Africa last month, including how it developed, how transmissible it is, and the severity of the disease caused by the strain compared to its predecessors, such as the Delta.

The S gene allows the formation of the virus’ spike protein, enabling it to penetrate human cells. The mutations show that “there can be cooperation between different parts of the virus,” Martin said in an interview.

According to the researcher, some of the hypotheses about its development include:

• the strain emerged in an area where genomic surveillance is low or people have little access to health care; or
• the strain could have developed in an immunosuppressed individual, who would have harbored the virus for a long period, allowing it to mutate; or
• the virus could have returned to an animal species, mutated, and then reinfected humans.

The World Health Organization (W.H.O.) and experts worldwide have repeatedly cautioned that the lack of access to vaccines in Africa and the inability of some countries to enforce them could lead to further mutations in the coronavirus.

Only 7% of the continent’s population of 1.2 billion people is fully vaccinated. The Democratic Republic of Congo, a nation of 100 million people, has immunized only 0.1% of its population, and Eritrea has yet to begin vaccination. In southern Africa, the high rate of HIV infections means that millions of people are immunosuppressed.

“We will only be able to distinguish between these hypotheses with further data,” the researchers said. “If one or more SARS-CoV-2 strains are detected as close relatives of the Omicron, then this would support the surveillance failure hypothesis.”

But if other variants are discovered in long-term human infections or in other animal species, these would support the other hypotheses, they said.