In mid-November, Tulio de Oliveira, who runs a genetics laboratory in South Africa, received anxious calls from doctors in the Eastern Cape province who are seeing explosive growth in Covid-19 patients. Hospitals were rapidly being overrun. The increase apparently came from nowhere.
“It was shocking,” said de Oliveira, a professor at the University of KwaZulu-Natal in Durban.
De Oliveira immediately asked for samples of the virus from the noses of patients so that he could genetically sequence it.
In less than a week, he compiled 16 samples. All 16 had similar mutations – and extremely many mutations.
“I said to myself, ‘here’s something very strange,'” de Oliveira said.
De Oliveira, a leading virus hunter, has discovered a new variant of the coronavirus.
The 16 samples were hundreds of kilometers apart in the provinces of Eastern Cape and KwaZulu-Natal, so he had a feeling that the variant was spreading fast.
To contribute to the concerns, there were some mutations in the genes associated with the nails that sit on top of the virus. Tests to detect the virus, as well as Covid-19 drugs and vaccines, targeted the nails. The concern is that it is possible that tests, drugs and vaccines may not work as well if the nails change.
One of the laboratories was in Stellenbosch, a town where South Africa’s famous wine cellars live.
De Oliveira said Susan Engelbrecht, the senior scientist at the Stellenbosch laboratory, told him she would be shocked if the new variant reached her area, as it is more than 700 kilometers from Nelson Mandela Bay, where the distribution of the variant first spotted.
“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 de Oliveira. “She said she would not only give me a bottle of wine, but that she would also eat her hat.”
Of the 67 samples from Stellenbosch, 58 were the same variant found in Nelson Mandela Bay.
De Oliveira is considering which Stellenbosch wine he will choose, but he knows it will be expensive.
A few days later, on December 4, de Oliveira sent an urgent e-mail 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 the agenda today – to issue a warning about some preliminary findings from South Africa,” de Oliveira wrote.
Permission was granted and de Oliveira warned the other scientists on the call, who were from all over the world, about this strange new variant he had seen in South Africa. He noted that this includes a mutation in a position of the vein protein called N501Y, and he encouraged his colleagues to look for similar mutations in their countries.
Maria Van Kerkhove, the technical leader for the WHO’s coronavirus response, said that the discovery of de Oliveira “is definitely caused [British scientists] to look at the different types of variants. ‘
‘I’m just so grateful we have it [international] cooperation, ”she said.
‘We are playing a very dangerous game with this virus’
If a virus changes its genetics in the right way, it cannot be detected so easily with tests and vaccines may not work as well.
“We are currently playing a very dangerous game with this virus,” Van Kerkhove said, given the explosive growth in the United States and other countries. “What worries us is that the longer it spreads, the more opportunities it has to change.”
These variants have been found in South Africa and the United Kingdom, but it is not clear where they started. So far it seems that both spread faster, but that they are not more lethal. Vaccines and other scientists are investigating whether the variants are a challenge for the vaccines.
Monitoring the virus – genetic sequencing of samples from large numbers of people – is ‘a fundamental aspect of fighting the virus’ and an important way ‘to understand your enemy’, Van Kerkhove said.
“The order really clinched it,” Bedford said.
Sequence of coronavirus in USA
On December 20, the day British scientists published their findings, a Slack group set fire to American virus hunters.
Perhaps the UK and South Africa’s variants or other worrying mutations also existed in the United States.
Looking at other countries, such as the United Kingdom and South Africa, can perform very well on genomic sequencing, Bedford said.
“Of course it’s frustrating,” he said.
After de Oliveira received the tip from doctors that the number of cases was growing, South Africa took only two weeks to identify the new variant. After British researchers received the fee from de Oliveira, it took them less than three weeks to find their own variant and publish their study.
Things are not moving that fast in the US, Bedford said.
In the United States, laboratories with coronavirus samples from patients often do not work directly with the scientists who will sequence the samples. This means that scientists have to identify those labs, ask them to store samples and then make legal agreements for sharing the samples.
‘Part of the reason we do such a bad job is that we did it. [these] structural issues, ”said Bedford.
South Africa and the United Kingdom, on the other hand, have national health services, so the laboratories that do Covid-19 testing and the experts that do sequencing usually work for the same entity.
“They have a single national health system and a single national microbiology service, which greatly facilitates the coordination of things,” said Dr. Gregory Armstrong, director of the Office of Advanced Molecular Detection at the CDC’s National Center for Emerging and Zoonotic Infections, said. Illnesses. “We do not have a system that is nearly as strong as the British system.”
Another reason why the US is lagging behind is that the UK has invested a lot of money in genomic order.
“The system in the UK is really the gold standard for how to do genomic surveillance,” Armstrong said. “I do not think we will ever be able to get to that level.”
The goal of the CDC is to double the number of coronavirus genomes in the U.S., Armstrong said. The sequencing is done in laboratories at the CDC, state health departments, universities and private enterprises.
The U.S. now tracks about 3,000 samples a week, and the CDC hopes it will more than double in the next two weeks to about 6,500 a week, he said.
Scientists around the world are eager to see the change.
“I am optimistic that it will get better quickly,” Van Kerkhove said.