Omicron: How deadly is the new variant from South Africa?

It’s still early days and most cases related to the new variant are based in one province in South Africa but the warning bells have started to ring as the whole world takes notice of the new covid variant. The variant harbors a large number of the mutations found in other variants, including Delta, and it seems to be spreading quickly across South Africa. A top priority is to follow the variant more closely as it spreads: it was first identified in Botswana earlier this month and has since turned up in a traveler arriving in Hong Kong from South Africa. Immediately there are questions around how quickly the new variant spreads, its ability to bypass some of the protection given by vaccines and what should be done about it.
“The world should provide support to South Africa and Africa and not discriminate or isolate it,” said Prof Tulio de Oliveira, the Durban-based scientist leading efforts to understand the new variant. Scientists are also trying to understand the variant’s properties, such as whether it can evade immune responses triggered by vaccines and whether it causes more or less severe disease than other variants do.
On 26 November, the World Health Organization (WHO) designated the strain, known as B.1.1.529, as a variant of concern and named it Omicron, on the advice of scientists who are part of the WHO’s Technical Advisory Group on SARS-CoV-2 Virus Evolution. Omicron joins Delta, Alpha, Beta and Gamma on the current WHO list of variants of concern.
Researchers also want to measure the variant’s potential to spread globally — possibly sparking new waves of infection or exacerbating ongoing rises being driven by Delta. Origin of the variant This variant was first reported to the World Health Organization from South Africa on 24 November 2021.
The epidemiological situation in South Africa has been characterized by three distinct peaks in reported cases, the latest of which was predominantly the Delta variant. In recent weeks, infections have increased steeply, coinciding with the detection of the B.1.1.529 variant. The first known confirmed B.1.1.529 infection was from a specimen collected on 9 November 2021. This variant has a large number of mutations, some of which are concerning. Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other VOCs.
There are a number of studies underway and the Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE) will continue to evaluate this variant. WHO will communicate new findings with Member States and to the public as needed.
Researchers spotted B.1.1.529 in genome- sequencing data from Botswana. The variant stood out because it contains more than 30 changes to the spike protein — the SARS-CoV-2 protein that recognizes host cells and is the main target of the body’s immune responses. Many of the changes have been found in variants such as Delta and Alpha, and are linked to heightened infectivity and the ability to evade infection-blocking antibodies.
The apparent sharp rise in cases of the variant in South Africa’s Gauteng province — home to  Johannesburg — is also setting off alarm bells. Cases increased rapidly in the province in November, particularly in schools and among young people, according to Richard Lessells, an infectious- diseases physician at the University of KwaZulu-Natal in Durban, South Africa.
What do South Africans have to say? Angelique Coetzee, the chairwoman of the South African Medical Association said that the new Omicron variant of the coronavirus results in mild disease, without prominent syndromes. “It presents mild disease with symptoms being sore muscles and tiredness for a day or two not feeling well. So far, we have detected that those infected do not suffer loss of taste or smell. They might have a slight cough.
There are no prominent symptoms. Of those infected some are currently being treated at home,” Coetzee said. The South African authorities said that South Africa is being “punished” for detecting a new Covid-19 variant Omicron. The ministry pointed out that new variants had been discovered in other parts of the world. “Each of those cases had no recent links with Southern Africa, but the reaction to those countries is starkly different to cases in Southern Africa,” it said.
The decision by a number of countries around the world to ban flights from southern Africa following the discovery of the variant “is akin to punishing South Africa for its advanced genomic sequencing and the ability to detect new variants quicker,” the foreign affairs ministry said in a statement.
Government insisted that South Africa’s “capacity to test and its ramped-up vaccination programme, backed up by a world-class scientific community should give our global partners the comfort that we are doing as well as they are in managing the pandemic”.
Meanwhile, Sixty-one people who arrived in Amsterdam on two flights from South Africa have tested positive for Covid-19, Dutch officials say. They have been placed in isolation at a hotel near Schiphol airport. They were among some 600 passengers held for several hours after arrival while they were tested for the virus. Many countries around the world have restricted travel from the southern African region.
Response in India After this variant emerged in South Africa, Indian scientists and health experts have also ring the alarm bells saying that new waves of infection are anticipated and unless we act quickly and efficiently, the country will possibly see repeat waves. India has better tools in hand now compared to two years ago, said Vinod Scaria, scientist at CSIR- Institute of Genomics and Integrative Biology (IGIB). He added the country, however, had to improve its vaccination drive, public health measures, health infrastructure and genomic surveillance to be better prepared.
The variant has also led to considerable concerns about the Indian cricket team’s tour to South Africa next month with BCCI sources saying that any decision on the matter will be based on the government’s advice.
The ongoing India A tour of South Africa, featuring three unofficial Tests in Bloemfontein, could also be called off midway given the uncertain situation which has prompted several visiting sportspersons to seek a way out of the country.
What’s in store for the future? According to some experts, this variant seems to be more devastating than others, including the highly transmissible Delta variant. Scientists can’t predict how different mutations will behave when combined, but of particular worry to scientists is that the virus has some 32 mutations in its spike protein, which is what vaccines teach our immune system to recognize and target. Though precautionary measures have been taken since the detection of Omicron, it is still a long battle we have to fight till we are completely safe.
(Prashant Bharadwaj)