In mid-November, Tulio de Oliveira, who heads a genetics laboratory in South Africa, began to receive anxious calls from doctors in the Eastern Cape province who observed an explosive growth in patients with Covid-19. Hospitals were rapidly being invaded. The increase apparently came out of nowhere.
“It was shocking,” said Oliveira, a professor at the University of KwaZulu-Natal in Durban.
De Oliveira immediately asked for samples of patients’ nose viruses to genetically sequence them.
In less than a week, he sequenced 16 samples. All 16 had similar mutations – and an exceptionally high number of mutations.
“I said to myself, ‘There is something very strange here,'” said Oliveira.
Oliveira, a prominent virus hunter, discovered a new variant of the coronavirus.
The 16 samples were separated by hundreds of kilometers from each other in the Eastern Cape and KwaZulu-Natal provinces, so he had a hunch that the variant was spreading rapidly.
To raise concerns, some of the mutations were in the genes related to the tips that are located on top of the virus. Tests to detect the virus, as well as Covid-19 drugs and vaccines, target these peaks. The concern is that if the peaks change, it is possible that the tests, drugs and vaccines may not work as well.
One of the laboratories was in Stellenbosch, a city that houses the famous South African wineries.
De Oliveira said Susan Engelbrecht, the senior scientist at the Stellenbosch laboratory, said she would have been shocked if the new variant had reached her area, as it is more than 700 kilometers from Nelson Mandela Bay, where the variant’s spread was the first. visa.
“I made a bet with her that if we found the variant in more than 50% of the samples from Stellenbosch, she would give me a bottle of wine,” said Oliveira. “She said she would not only give me a bottle of wine, but she would also eat her hat.”
Of the 67 samples of Stellenbosch, 58 were the same variant found in Nelson Mandela Bay.
Oliveira is considering which Stellenbosch wine to choose – but he knows it will be expensive.
A few days later, on December 4, de Oliveira sent an urgent email to the World Health Organization official who runs the agency’s SARS-CoV-2 Virus Evolution Working Group.
“I would like to request an urgent addition to today’s agenda – to warn of some preliminary findings from South Africa,” wrote Oliveira.
Permission was granted, and Oliveira alerted other liaison scientists from around the world about this strange new variant he was seeing in South Africa. He noted that it included a mutation in a position of the spike protein called N501Y and encouraged his colleagues to look for similar mutations in their countries.
Maria Van Kerkhove, the technical leader for the response to the WHO coronavirus, said that Oliveira’s discovery “definitely triggered [British scientists] to see the different types of variants. ”
“I am so grateful that we have this [international] collaboration, “she said.
‘We are playing a very dangerous game with this virus’
If a virus changes its genetics in the right way, tests may not be able to detect it so easily and vaccines may not work as well.
“We are playing a very dangerous game with this virus now,” said Van Kerkhove, due to explosive growth in the United States and other countries. “What concerns us is that the longer it spreads, the more opportunities it has to change.”
These variants were found in South Africa and the United Kingdom, but it is not clear where they started. So far, it seems that both have spread more quickly, but are no longer deadly. Vaccine manufacturers and other scientists are studying whether the variants pose a challenge for vaccines.
Keeping an eye on the virus – sequencing samples genetically from a large number of people – is “a fundamental aspect of virus control” and an important way “to understand the enemy,” said Van Kerkhove.
“The sequencing is really over,” said Bedford.
Sequencing the coronavirus in the USA
On December 20, the day British scientists published their findings, a Slack group of virus hunters in the United States lit up.
Perhaps the UK and South Africa variants or other worrying mutations also exist in the United States.
Watching other countries, like the UK and South Africa, excelling in genomic sequencing can be difficult, Bedford said.
“Sure, it’s frustrating,” he said.
In South Africa, after Oliveira received information from doctors that the number of cases was growing, it took him and his colleagues just two weeks to identify the new variant. After British researchers received Oliveira’s tip, it took them less than three weeks to find their own variant and publish their study.
Things do not happen so quickly in the United States, Bedford said.
In the United States, laboratories that have coronavirus samples from patients often do not work directly with the scientists who will sequence these samples. This means that scientists need to identify these laboratories, ask them to keep samples and then make legal arrangements to share the samples.
“Part of the reason we’re doing such a bad job is that we have [these] structural issues, “said Bedford.
South Africa and the United Kingdom, on the other hand, have national health services, so the laboratories that test Covid-19 and the specialists who do the sequencing usually work for the same entity.
“They have a single national health system and a single national microbiology service, which makes it much easier to coordinate things,” said Dr. Gregory Armstrong, director of the Office of Advanced Molecular Detection at the CDC National Center for Infectious. Emerging and Zoonotic Diseases. “We don’t have a system as robust as the UK system.”
Another reason the US is lagging behind is that the UK has invested large sums of money in genomic sequencing.
“The system in the UK is really the gold standard for doing genomic surveillance,” said Armstrong. “I don’t think we’ll ever be able to reach that level.”
The CDC’s goal is more than doubling the number of coronavirus genomes sequenced in the U.S., said Armstrong. The sequencing is done in CDC laboratories, state health departments, universities and private companies.
The United States is now sequencing about 3,000 samples a week, and the CDC expects in the next two weeks to more than double to about 6,500 a week, he said.
Scientists around the world are eager to see the change.
“I am optimistic that this will improve quickly,” said Van Kerkhove.