Omicron variant highlights uneven genomic sequencing around the world – .

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Omicron variant highlights uneven genomic sequencing around the world – .


It was a sudden rise in coronavirus infections in South Africa’s Gauteng province from mid-November that first alerted scientists across the country to the emergence of a disturbing new variant – now identified as Omicron.

Health experts credit the rapid work of the South African scientific community, internationally recognized for its strong record in managing the HIV and TB epidemics, in identifying the new variant and taking action to alert the world.

But gaps in the global effort to track mutations, a process known as genomic sequencing, make it difficult not only to track early cases of Omicron, but also to identify future variants.

The tools needed for genome sequencing are concentrated in the wealthiest countries, which means that large parts of the globe are not being properly tracked. More than 80% of the more than 5 million Sars-Cov-2 genomes uploaded to the Gisaid genomic database, which promotes rapid sharing of coronavirus data, come from two continents: North America and Europe .

“We fly blindly over large areas of the world, many of which are under-vaccinated,” said Peter Bogner, founder of Gisaid. “This is most important in the areas where we are currently flying blind to make sure we have better vision. “

Omicron’s discovery follows a sharp rise in coronavirus cases in South Africa’s Guateng province © Bloomberg

Until recently, genome sequencing was a niche area of ​​research used primarily by academics and infectious disease experts.

The pandemic has changed that. The World Health Organization, which named Omicron a worrying variant a week ago, has identified genomic sequencing as a key weapon in the fight against a virus that has killed more than 5 million people worldwide.

“The public health benefits of the rapid and widely available genomic sequences of Sars-Cov-2 for monitoring viral evolution and the emergence of variants have become clearly clear,” said Soumya Swaminathan, chief scientist of the organization. global health.

Fortunately, a genomic quirk in the form of a missing gene means Omicron can be detected by PCR testing. And in sequencing, experts say, quality matters more than quantity.

“It’s not about numbers, it’s about understanding the epidemic, what it means,” said Tulio de Oliveira, professor of bioinformatics at Stellenbosch University whose team was the first to analyze the highly mutated genomes detected in Gauteng.

South Africa, he said, has been aided by a collaborative network of laboratories and scientists as well as strong support from the government. Importantly, although he only sequences a small proportion of samples, he does so strategically, he added.

“For example, Brazil, UK and India have up to 10,000 times more sequencing than we do. But in South Africa we have identified the two variants [the earlier Beta and Omicron] faster, ”he said. “If we find something that is spreading all over the place, in places hundreds of miles apart, we can draw solid conclusions such as a potential new variant increasing the prevalence. “

But experts admit that even if the rest of the world sought to increase their genome sequencing capabilities as a result, the lack of the necessary raw material, including the reagents needed to complete the process, would make it very difficult for them. so.

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Bogner said Western countries have not learned a lesson from the Alpha variant, which spread across southern England before spreading around the world last year.

“After Alpha, a lot of noise was made about the need for countries to improve their genome sequencing efforts,” Bogner said. “Countries like the United States and Germany, which performed dismally at the end of 2020, may have been a game-changer. But they overlooked the urgent need for low- and middle-income countries to get their hands on the reagents needed to generate data. “

The reagents, chemicals he described as “the fuel” for genomic sequencing technology, have been “cornered” by a small number of Western countries since the start of the pandemic.

De Oliveira said on Thursday that South Africa was dangerously short of reagents and had enough for the next three days. The shortage, as the world looked to South Africa for answers, was exacerbated by blanket travel bans imposed in the wake of Omicron’s discovery.

“It’s difficult because these reagents have a cold chain. When they’re stuck in an airport for days on end, you ruin the cold chain, ”said De Oliveira, comparing the mentality behind the flight bans imposed by Western countries to the hoarding of vaccines that left the population poorly vaccinated southern Africa open to new variants.

Even before Omicron, it was already “really hard to get reagents,” according to De Oliveira. He said wealthier countries almost boasted about the volume of sequencing tests they performed.

Francine Ntoumi, founder of the Congolese Foundation for Medical Research in Congo-Brazzaville, agrees.

She said genomic surveillance was most needed in countries with low vaccination rates. Countries where chronically ill patients cannot access vaccines were “still the most likely to speed up adaptation and progression of the virus.”

An electronic pipette from the SpiceHealth genome sequencing laboratory installed at an airport in New Delhi, India, where a laboratory has been set up to test positive samples in search of new variants.
Health experts say there is a need to increase genomic sequencing capacity worldwide, but lack of reagents hampers such efforts in poorer countries © 2021 Bloomberg Finance LP

Before Omicron’s arrival, Ntoumi’s lab, which sequenced around 300 Sars-Cov-2 genomes in total, was the first to discover a variant, dubbed B.1.640, which also had a series of cutting-edge mutations. unusual.

“B.1.640 should have been a harbinger of what was to come with Omicron,” she said.

“In my lab, we have two sequencers but they are not well used”, explains Ntoumi. “We can do three times more sequences than we do and with that, we would be able to do reliable genomic monitoring for the whole of Congo-Brazzaville. “

Bogner said he witnessed the inequality of genomic surveillance from the data center at Gisaid’s California headquarters.

“We have a room which is a visual sorting area, where data flows in,” he said. “When a dozen genome sequences are received from countries that have historically reported very little, our curators rejoice. When they see 20,000 genomes generated by a major US government contractor, their response is not the same.

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