Omicron: All about 'highly transmissible' South Africa Covid variant that has put India on alert

Omicron Covid Variant: Amid COVID-19 third wave scare, a new variant of novel coronavirus 'Omicron' has been detected in South Africa. The detection of the new Covid variant has put many countries, including India, on high alert. Hours after the announcement, the Centre issued an advisory to states, UTs for international travellers from specified countries. 

The Centre has asked all states and Union Territories to conduct rigorous screening and testing of all international travellers coming from or transiting through South Africa, Hong Kong and Botswana, where a new COVID-19 variant of serious public health implications has been reported.

United Kingdom, Germany and Italy have also banned travel from South Africa to contain the spread of new Covid variant. France too has suspended all flights coming from southern Africa for 48 hours

Omicron​: 'Highly transmissible' New Covid Variant B.1.1.529

It's unclear from where the new variant classed as B.1.1.529 actually arose, but it was first detected by scientists in South Africa. A newly identified COVID-19 variant --- B.1.1.529 --- is causing an increase in new COVID-19 infections in South Africa. The country recorded its 22 cases following genomic sequencing collaborations. The new variant has also been detected in neighbouring Botswana and as far away as Hong Kong. However, the new variant has not been found in India so far.

Scientists, the world over will be watching the new variant for signs of gaining momentum or spreading more widely and rapidly. The high number of spike mutations are concerning from the point of view of both higher transmissibility and immune evasion.

Indian-origin professor of clinical microbiology at Cambridge University, Ravi Gupta, told The Guardian newspaper that work in his laboratory found that two of the mutations on B.1.1.529 increased infectivity and reduced antibody recognition.

Why are scientists worried about this new variant?

It appears to have a high number of mutations — about 30 — in the coronavirus’ spike protein, which could affect how easily it spreads to people.

Sharon Peacock, who has led genetic sequencing of COVID-19 in Britain at the University of Cambridge, said the data so far suggest the new variant has mutations “consistent with enhanced transmissibility,” but said that “the significance of many of the mutations is still not known.”

Lawrence Young, a virologist at the University of Warwick, described omicron as “the most heavily mutated version of the virus we have seen,” including potentially worrying changes never before seen all in the same virus.

Dr. Anthony Fauci, the U.S.′ top infectious diseases doctor, said American officials had arranged a call with their South African counterparts later on Friday to find out more details and said there was no indication the variant had yet arrived in the U.S.

What's know and not known about the variant?

Scientists know that omicron is genetically distinct from previous variants including the beta and delta variants, but do not know if these genetic changes make it any more transmissible or dangerous. So far, there is no indication the variant causes more severe disease.

It will likely take weeks to sort out if omicron is more infectious and if vaccines are still effective against it.

Peter Openshaw, a professor of experimental medicine at Imperial College London said it was “extremely unlikely” that current vaccines wouldn’t work, noting they are effective against numerous other variants.

Even though some of the genetic changes in omicron appear worrying, it’s still unclear if they will pose a public health threat. Some previous variants, like the beta variant, initially alarmed scientists but didn’t end up spreading very far.

“We don’t know if this new variant could get a toehold in regions where delta is,” said Peacock of the University of Cambridge. “The jury is out on how well this variant will do where there are other variants circulating.” To date, delta is by far the most predominant form of COVID-19, accounting for more than 99% of sequences submitted to the world’s biggest public database.

How did this new Covid variant arise?

The coronavirus mutates as it spreads and many new variants, including those with worrying genetic changes, often just die out. Scientists monitor COVID-19 sequences for mutations that could make the disease more transmissible or deadly, but they cannot determine that simply by looking at the virus.

They must compare the pattern of disease in outbreaks to the genetic sequences and sorting out whether there is an actual connection can take time.

Some scientists have speculated that the new variant arose in an immune-compromised patient because of the large number of mutations.

Sharon Peacock, who has led genetic sequencing of COVID-19 in Britain at the University of Cambridge, said the variant “may have evolved in someone who was infected but could then not clear the virus, giving the virus the chance to genetically evolve," in a scenario similar to how experts think the alpha variant — which was first identified in England — also emerged.

Are the travel restrictions being imposed by some countries justified?

Maybe. As of noon Friday, travelers arriving in the U.K. from South Africa, Namibia, Botswana, Lesotho, Eswatini and Zimbabwe will have to self-isolate for 10 days. European Union nations also moved quickly on Friday to ban air travel from southern Africa, and the U.S. also said it would ban travel from South Africa and seven other African nations by non-US citizens beginning Monday.

Given the recent rapid rise in COVID-19 in South Africa, restricting travel from the region is “prudent” and would buy authorities more time, said Neil Ferguson, an infectious diseases expert at Imperial College London.

Jeffrey Barrett, director of COVID-19 Genetics at the Wellcome Sanger Institute, thought that the early detection of the new variant could mean restrictions taken now would have a bigger impact than when the delta variant first emerged

“With delta, it took many, many weeks into India’s terrible wave before it became clear what was going on and delta had already seeded itself in many places in the world and it was too late to do anything about it,” he said. “We may be at an earlier point with this new variant so there may still be time to do something about it.”

WHO classifies new variant as 'highly transmissible' virus of concern

World Health Organization on Friday classified the new COVID-19 variant as a 'highly transmissible' virus of concern, first detected in South Africa as a highly transmissible virus of concern and named it "omicron" under its Greek-letter system. The announcement Friday from the United Nations health agency marks the first time in months that WHO has classified a COVID-19 variant as such. The delta variant, which has become the world's most prevalent, is in the same category.

The advisory panel classified as a “variant of concern” — the most worrying type, like the well-known delta variant — or a “variant of interest," and whether to use a Greek letter to classify it.

What happens next?

The World Health Organization convened a technical group of experts to assess the South African data and to decide whether the new variant warrants being designated a variant of interest or a variant of concern.

Variants of interest — which currently include the mu and lambda variants — have genetic changes known to affect things like transmissibility and disease severity and have been identified to cause significant clusters in multiple countries.

Variants of concern — which include alpha, beta and delta — have shown they can spread more easily, cause more serious disease or make current tools like vaccines less effective.

To date, the delta variant remains by far the most transmissible form of COVID; it accounts for more than 99 per cent of sequences shared with the world's biggest public database.

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