Omicron: the pandemic book’s next chapter

Just as the world’s begun to reopen, a new SARS-CoV-2 variant has emerged to disrupt many people’s Christmas travel plans. But the emergence of the B.1.1.529 (Omicron) variant, first discovered in Botswana on 11 November, is not at all surprising.

For months, experts have warned that the longer the virus is let run rampant in any part of the world, the higher the likelihood of new, potentially more dangerous variants emerging.

But vaccine hoarding and the lack of a global plan have meant that while wealthy countries like Australia are rolling out third doses, vaccine rates remain extremely low and the virus’s spread uncontrolled in other parts of the world.

The situation in Botswana

In Botswana, only 20% of the population is fully vaccinated, and the country is on the tail of a Delta wave. Like other southern African countries, Botswana has a high rate of HIV infections, which scientists have warned could drive SARS-CoV-2 mutations.

There is good evidence that people with weakened immune systems, such as those living with HIV, are more likely to remain infected with COVID-19 for several weeks. Prolonged infection is one of the mechanisms for the emergence of variants.

A study, published as a preprint last June, reported a 36-year-old woman with advanced HIV who carried SARS-CoV-2 for 216 days, during which the virus accumulated more than 30 mutations.

Out of the 37.7 million people living with HIV worldwide, over 65% live in sub-Saharan Africa, and around 8 million of them do not receive effective antiretroviral therapy: the perfect breeding ground for the B.1.1.529 variant to emerge.

Omicron named

On Friday 26 November, the WHO named the new variant with the Greek letter Omicron and classified it as a variant of concern.

Principal among WHO’s concerns are the large number of mutations on the spike the virus uses to attach to our cells, some of which are linked to increased transmissibility.

But in an update released last Sunday, the WHO said it is not yet clear whether Omicron spreads more easily from person to person or causes more severe disease than other variants. It might take weeks for scientists to gather robust evidence.

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Researchers estimated that the R0 – the average number of new cases caused by each infection – was 1.47 in South Africa.

Preliminary data suggest that Omicron might be more transmissible but cause milder disease. But reported infections in Africa were among university students – younger individuals who tend to have milder disease.

It’s also still unclear whether current vaccines will be effective against Omicron. Moderna is already testing two booster candidates in the clinic designed to anticipate mutations, and one of the candidates includes several mutations present in the Omicron variant. The company is expecting Omicron-specific booster candidates to be ready for clinical testing in two or three months.

So far, vaccines designed against the original strain have held well against new variants with reduced effectiveness against infection rather than severe disease.

What happens elsewhere?

While the world waits to understand more about how Omicron behaves, several countries, including Australia, the US, Canada, the UK, Europe, Hong Kong and Japan, announced almost immediate travel bans from southern African nations.

But even if Omicron is more transmissible than Delta, travel bans would only slow, not stop the importation of the new strain, tweeted Associate Professor Adam Kucharski, an infectious disease epidemiologist at the London School of Hygiene and Tropical Medicine.

The variant has already been reported in multiple countries other than Africa, including five cases in Australia. 

In a BBC interview gone viral, Dr Ayoade Alakija, co-chair of the African Vaccine Delivery Alliance, said the emergence of a new variant was “absolutely inevitable” because the world has failed to vaccinate countries equitably. She said wealthy countries who have hoarded vaccines now want to keep Africans out.

“It is the result of the world’s failure to vaccinate in an equitable, urgent and speedy manner,” Alakija says. “It is the result of hoarding by high-income countries of the world. These travel bans are based on politics and not on science. It is wrong.

“Until everyone is vaccinated, no one is safe. But what exactly is the global playbook on this? What are we planning to do? Knee-jerk reactions so that we can satisfy those people within our countries that we’re keeping those unvaccinated Africans out? Why are Africans unvaccinated?

“We knew we were going to get here. We knew this is where the hoarding, the lack of IP waivers, the lack of cooperation on sharing tech and know-how was going to bring us to. Why are we acting surprised?”

Omicron has emerged in a continent where only 10% of the 1.2 billion total population have received one dose of a COVID-19 vaccine. Dr Vinod Balasubramaniam, a virologist at the Jeffrey Cheah School of Medicine & Health Sciences at Monash University in Malaysia, said every time the virus replicates in someone’s body, there is a chance of it mutating in a new variant. “This is a numbers game,” he says. “If we don’t address [vaccine inequity] quickly enough, our exit from the pandemic will be set back, possibly for months or years on end.”