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How South African Scientists Spotted The Omicron COVID Variant

A laboratory in South Africa sequenced the genes on eight coronavirus samples, which led to the discovery of the Omicron variant.

How South African Scientists Spotted The Omicron COVID Variant
South African scientists sequenced the genes on eight coronavirus samples at a laboratory to discover the Omicron variant
Highlights
  • President Cyril Ramaphosa is considering introducing mandatory vaccination
  • Daily COVID-19 infection rate is expected to quadruple to more than 10,000
  • Samples, tested all bore a large number of mutations: Lancet laboratory

Johannesburg: On Friday, November 19, Raquel Viana, Head of Science at one of South Africa’s biggest private testing labs, sequenced the genes on eight coronavirus samples – and got the shock of her life. The samples, tested in the Lancet laboratory, all bore a large number of mutations, especially on the spike protein that the virus uses to enter human cells. “I was quite shocked at what I was seeing. I questioned whether something had gone wrong in the process,” she told Reuters, a thought that quickly gave way to “a sinking feeling that the samples were going to have huge ramifications”.

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

I didn’t quite know how to break it to them,” she recalls. She told Amoako, To me, it looks like a new lineage.

The discovery of the Omicron variant in southern Africa has caused global alarm, with countries limiting travel from the region and imposing other restrictions for fear it could spread quickly even in vaccinated populations.

Also Read: India Detects First 2 COVID-19 Cases Of Omicron Variant In Karnataka, Government Asks To Not Panic

Amoako and the team at the NICD spent the Nov. 20-21 weekend testing the eight samples which Viana sent them, all of which had the same mutations, he told Reuters on Tuesday.

It was so bizarre that Amoako, his colleague Josie Everatt and other colleagues also thought it must be a mistake. Then they remembered that over the week, they’d noticed a sharp rise in COVID-19 cases, of the sort that might indicate a new mutant.

In addition, Viana had been alerted to an oddity in the sample earlier this month by a colleague – an S-gene dropout, one of the mutations that now distinguishes the new Omicron variant of the coronavirus from the globally dominant Delta one.

The only common variant with that feature was Alpha, “and we hadn’t seen Alpha (in South Africa) since August,” Everatt recalls thinking as they tested the samples.

By Tuesday, Nov. 23, after testing another 32 from around Johannesburg and Pretoria, It was clear, Amoako said. It was scary Amoako said.

Also Read: Omicron Variant Could Outcompete Delta, Says South African Disease Expert

Burning Questions

On the same Tuesday, the NICD team informed the department of health and other labs across South Africa doing sequencing, which later started coming up with similar results.

The same day, the NICD entered the data into the GISAID global science database, and found that Botswana and Hong Kong had also reported cases with the same gene sequence.

On Nov. 24, NICD officials and the department notified the World Health Organisation.

By that stage, Viana said, more than two-thirds of positive tests in Gauteng, the South African province that includes Pretoria and Johannesburg, were showing the S-gene dropout – a sign that Omicron was already becoming dominant.

Thanks to Omicron, South Africa’s daily COVID-19 infection rate is expected to quadruple to more than 10,000 by the end of this week, one of the country’s leading infectious disease specialists, Salim Abdool Karim, said on Monday.

Also Read: Toxic Mix Of Low COVID-19 Vaccination And Testing A Recipe For Amplifying Variants: WHO Chief

The important questions – how good is the new variant at evading immunity from vaccines or past illness, how severe are the symptoms, compared with previous versions, and how will this differ among age groups – remain to be answered.

Three scientists interviewed by Reuters who are working on those questions expect answers in about 3-4 weeks.

In the meantime, South African President Cyril Ramaphosa is considering introducing mandatory vaccination in some contexts, with the country still reeling from 3 million COVID-19 infections in total during the pandemic and over 89,000 deaths.

There is much anger in South Africa at the foreign travel bans – some of it directed at the scientists. Amoako receives some angry messages saying they should just “stop looking” for new variants.

Wolfgang Preiser, a virologist at Stellenbosch University working on COVID-19, who also has received hate mail, worries that other countries might take this whole saga as a lesson not to be so transparent.

It might encourage other countries to hide things, or rather, just not to look, said Presier. That’s the fear. Looking is quite an investment, so maybe they will conclude, ‘let’s not bother’.

Also Read: Genome Sequencing Can Confirm Presence Of COVID-19 Variant Omicron: Expert

(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)

NDTV – Dettol have been working towards a clean and healthy India since 2014 via Banega Swachh India initiative, which is helmed by Campaign Ambassador Amitabh Bachchan. The campaign aims to highlight the inter-dependency of humans and the environment, and of humans on one another with the focus on One Health, One Planet, One Future – Leaving No One Behind. It stresses on the need to take care of, and consider, everyone’s health in India – especially vulnerable communities – the LGBTQ populationindigenous people, India’s different tribes, ethnic and linguistic minorities, people with disabilities, migrants, geographically remote populations, gender and sexual minorities. In wake of the current COVID-19 pandemic, the need for WASH (WaterSanitation and Hygiene) is reaffirmed as handwashing is one of the ways to prevent Coronavirus infection and other diseases. The campaign will continue to raise awareness on the same along with focussing on the importance of nutrition and healthcare for women and children, fight malnutrition, mental wellbeing, self care, science and health, adolescent health & gender awareness. Along with the health of people, the campaign has realised the need to also take care of the health of the eco-system. Our environment is fragile due to human activity,  that is not only over-exploiting available resources, but also generating immense pollution as a result of using and extracting those resources. The imbalance has also led to immense biodiversity loss that has caused one of the biggest threats to human survival – climate change. It has now been described as a “code red for humanity.” The campaign will continue to cover issues like air pollutionwaste managementplastic banmanual scavenging and sanitation workers and menstrual hygiene. Banega Swasth India will also be taking forward the dream of Swasth Bharat, the campaign feels that only a Swachh or clean India where toilets are used and open defecation free (ODF) status achieved as part of the Swachh Bharat Abhiyan launched by Prime Minister Narendra Modi in 2014, can eradicate diseases like diahorrea and the country can become a Swasth or healthy India.

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