By Tim Cocks

JOHANNESBURG, (Reuters) – On Friday, Nov. 19, Raquel Viana, Head of Science in one of South Africa’s largest private testing laboratories, sequenced eight coronavirus genes – and received the shock of her lifetime.

Tested in the Lancet laboratory, the samples showed many mutations. This was especially true for spike protein which the virus uses to enter the human body.

“I was very shocked by the things I was seeing. “I was quite shocked at what I saw.” She told Reuters that she questioned if something went wrong during the process. This thought soon gave way to the sinking sensation that the samples could have serious ramifications.

He was Daniel Amoako, a gene sequencer at the National Institute for Communicable Diseases (NICD), in Johannesburg. She picked her phone up quickly.

She recalls that she didn’t know how to explain it to them. Amoako said that it looked like a brand new lineage to her.

Global alarm was raised by the discovery of Omicron in Southern Africa. Countries have restricted travel to the area and placed other restrictions in fear that it might spread rapidly, even among vaccinated people.

Amoako spent Saturday, Nov. 20-21, with the NICD team, testing eight of Viana’s samples. All had identical mutations.

Amoako and Josie Everatt (his colleague) thought that it was a mistake. They remembered they had noticed an increase in COVID-19-related cases over the past week. This might have been a sign of a new mutation.

Viana also discovered an anomaly in Viana’s sample by a coworker earlier this month. It was an S-gene Dropout. One of the mutations which now differentiates the Omicron coronavirus variant from the Delta dominant one.

Everatt recalls that Alpha was the only variant of this feature in common. “And we hadn’t seen Alpha (in South Africa), since August,” Everatt thought as Everatt tested the samples.

Amoako claimed that it had been clear by Tuesday, 23 November after testing 32 additional samples from Johannesburg or Pretoria.

It was frightening.

Questions about BURNING

The NICD team also informed South Africa’s department of health, along with other laboratories in South Africa, about the Tuesday’s sequencing results. These labs later came up with identical results.

The NICD also entered the data in the GISAID global scientific database. They found that Botswana had already reported the same case as Hong Kong.

Officials from the NICD and the department notified World Health Organisation on November 24.

Viana stated that by that point, over two-thirds (or more) of the positive Gauteng tests, which includes Pretoria, Johannesburg and Johannesburg were showing S-gene dropout, which was a signal that Omicron was becoming increasingly dominant.

Omicron is expected to triple South Africa’s COVID-19 daily infection rate to over 10,000 this week. This was according to Salim Abdool Karim (one of the nation’s most respected infectious disease specialists), Monday.

It remains to be determined how effective the new variant is at hiding immunity against past or present illness. How severe are symptoms, relative to the previous version, and how this will differ between ages.

Three scientists interviewed for Reuters expect to receive answers within three to four weeks by the researchers who worked on these questions.

South African President Cyril Ramaphosa considers introducing compulsory vaccinations in certain situations, as the country continues to reel from over 3 million COVID-19 infection during the pandemic.

South Africa’s ban on foreign travel is causing anger. Amoako is bombarded with angry messages urging him and his colleagues to “stop searching” for better variants.

Wolfgang Preiser (a Stellenbosch University virusologist working on COVID-19) worries about the possibility that countries will take this story as an example of transparency.

He said, “It could encourage other countries hide things or just not look.”

That’s what they fear. They might conclude that it is worth the effort to look.