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In-Depth | Omicron: All you need to know about new COVID-19 strain from South Africa

In-Depth | Omicron: All you need to know about new COVID-19 strain from South Africa

India has, so far, not reported any case of B.1.1.529 variant, official sources have said. The Centre has asked states and UTs for rigorous screening and testing of travellers from or transiting through South Africa, Hong Kong and Botswana

Researchers in South Africa are racing to get ahead of a new coronavirus variant that is spreading in the country after it was first detected in the neighbouring Botswana.

Called B.1.1.529, the new strain, which has a number of mutations seen in the variants such as the Delta, could be spreading quickly across the country, adding to the urgency to track its spread. The World Health Organisation (WHO) has named it Omicron has designated it as a Variant of Concern. A variant of concern is the WHO's top category of worrying COVID-19 variants.

Scientists are looking to determine how resistant the new strain is to vaccines, the chances of re-infection in vaccinated individuals and if it causes more severe disease.

Penny Moore, virologist at the University of Witwatersrand, Johannesburg, whose lab is studying the new variant’s potential to dodge vaccines and re-infect, told Nature they are “flying at warp speed” and while they do have anecdotal reports, “it is too early to tell anything”.

South Africa, with a population of 60 million, has, so far, recorded more than 2.9 million COVID-19 cases, including over 89,000 deaths.

Not just South Africa, the entire world is on the defensive about this new strain after the Delta variant swept across the globe, triggering new COVID-19 waves.

Vaccination in South Africa

Here is all you need to know about B.1.1.529, dubbed as Omicron

– First identified in Botswana, the strain has been found in travellers to Hong Kong from South Africa and labelled B.1.1.529.

– At present, a bulk of the cases are concentrated in the South African province of Gauteng and its capital Johannesburg. This is also the country's most populous province, according to health minister Joe Phaahla.

– Professor Tulio de Oliveira, a bioinformatician at the University of KwaZulu-Natal, said his team found that the variant was responsible for all of 77 of the virus samples collected from Gauteng between November 12 and 20 and analysed. Another 100 samples are also being examined.

– The new coronavirus variant was first detected in May and has now spread to most South African provinces and Britain, Germany, Italy, the Netherlands, Denmark, Belgium, Botswana, Israel, Australia and Hong Kong.

– South Africa's National Institute for Communicable Diseases in a statement said: "Although the data are limited, our experts are working overtime with all the established surveillance systems to understand the new variant and what the potential implications could be.”

– Phaahla said the country as a whole has seen a dramatic and exponential rise in new infections over the last four or five days, where “the new variant appears to be driving the spike in cases”. Notably, numbers jumped in the past week from 200 new cases a day to 1,200 on November 24 and 2,645 on November 25.

– The Omicron coronavirus variant kept spreading around the world on Sunday, with 13 cases found in the Netherlands and two each in Denmark and Australia. Dutch health authorities said the 13 cases of the variant were found among people on two flights that arrived in Amsterdam from South Africa on Friday. Denmark said it had registered two cases in travelers from South Africa, while officials in Australia said two passengers who arrived in Sydney from southern Africa had tested positive for the variant.

– The COVID-19 variant that emerged in South Africa was named after the 15th letter of the Greek alphabet. Some other variants with Greek letters do not reach those classification levels, and the WHO also skipped two letters just before omicron — “nu” and “xi” — leading to speculation about whether “xi” was avoided in deference to the Chinese president, Xi Jinping, the New York Times reported.

Tarik Jasarevic, a spokesperson said that 'Nu' is too easily confounded with ‘new' and ‘xi’ was not used because it is a common last name. He added that the agency’s best practices for naming diseases suggest avoiding “causing offense to any cultural, social, national, regional, professional or ethnic groups.”

– There are now seven “variants of interest” or “variants of concern,” and they each have a Greek letter, according to a WHO tracking page. 

11 virus mutation

What are the mutations?

– Genome sequencing of the B.1.1.529 variant first raised concern after researchers found over 30 changes to the spike protein. (The SARS-CoV-2 spike protein recognises host cells and is the main target of immune responses).

– Reports said that due to the sheer number of mutations, this variant is most radically different to the one that emerged in Wuhan, China in late 2019, triggering the pandemic.

– In a media briefing de Oliveira said the variant showed a total of 50 mutations, of which 30 were protein spike mutations. They got the numbers from a single patient who succumbed to the virus.

– Further, the receptor-binding domain (which allows the virus to make first contact with host body cells) has 10 mutations, compared to two seen in the Delta variant.

– Many changes are setting off alarm bells as similar spikes in the Alpha and Delta variants were found to increase infection rate and ability to block vaccines/antibodies.

– Moore said there are hints that mutations could contribute to the virus’ evasion of vaccine and antibodies, even from T cells, which play a vital role in providing immunity. Her team had also provided some of the first data on the Beta variant’s ability to dodge immunity. Her team hopes to have its first results on Omicron (B.1.1.529) in two weeks.

Tedros Ghebreyesus_sep30

WHO response

– A WHO team, which is monitoring the new variant, and its Technical Advisory Group on Virus Evolution (TAG-VE) met on November 26 to discuss the level of concern for the strain.

– While it was earlier speculated that they were likely to dub the new strain ‘Nu’ based on the Greek naming system adopted by WHO, the organisation finally named the new strain 'Omicron'.

– Dr Maria Van Kerkhove, WHO’s technical lead on COVID-19, said they do not know much about the new strain but “we do know is that this variant has a large number of mutations and the concern is that when you have so many mutations, it can have an impact on how the virus behaves”.

– The WHO Regional Director for Africa, Matshidiso Moeti, also criticised some of the travel bans targeting African countries as divisive, and urged countries to follow science and international health regulations in their decision-making.

"With the Omicron variant now detected in several regions of the world, putting in place travel bans that target Africa attacks global solidarity," she said in a statement.

Covid travel aeroplane male steward lukas-souza-5KRFOTnpnnY-unsplash

Global travel curbs

– The United Kingdom on November 26 said it will add six countries to its ‘red list’ and temporarily ban flights, BBC reported. This comes despite no confirmed cases of the variant in the UK.

– All flights from South Africa, Namibia, Zimbabwe, Botswana, Lesotho and Eswatini are being suspended and UK Health Secretary Sajid Javid “scientists are deeply concerned" but need to learn more.

– Javid said the more is “being cautious and taking action to protect our borders as best we can”. The UK removed all countries from its red list in October. Around 500-700 people travel to the isles from South Africa daily and this number is likely to increase due to the holidays.

– Scotland, too, is following the UK and making anyone arriving from the six countries to self-isolate and take two PCR tests. Hotel quarantine is also being implemented.

– In the most far-reaching effort to keep the variant at bay, Israel announced late on Saturday it would ban the entry of all foreigners and reintroduce counter-terrorism phone-tracking technology to contain the spread of the variant. Prime Minister Naftali Bennett said the ban, pending government approval, would last 14 days. Officials hope that within that period there will be more information on how effective vaccines are against Omicron.

– The top US infectious disease official, Anthony Fauci, said Americans should be prepared to fight the spread of the new variant, but that it was not yet clear what measure such as mandates or lockdowns would be needed. He has said the variant is likely already in the country, although no cases have been confirmed.

– However, Mexico's deputy health secretary, Hugo Lopez Gatell, said travel restrictions are of little use, calling measures taken by some countries "disproportionate".

– Meanwhile, South Africa itself will remain on the lowest 'Level One' of its five-level lockdown strategy to fight the Covid-19 pandemic despite the global panic around the detection of the Omicron variant in the country, President Cyril Ramaphosa announced.

Ramaphosa also called on more than 20 countries that have imposed travel bans to and from South Africa and its neighbours to immediately end the ban to avoid further harm to the economies of these countries, which have already been battered by the pandemic. Stating: "(The ban) is a clear and completely unjustified departure from the commitment that many of these countries made at the meeting of G20 countries in Rome last month."

– Till date, European countries along with the UK have banned travel to and from South Africa and neighbouring countries of Namibia, Zimbabwe and Botswana, as well as Lesotho and Eswatini (formerly Swaziland), both of which are landlocked within South Africa. Other countries include Mauritius, Israel, Sri Lanka, Pakistan, the US, Canada and the Netherlands. Japan is also considering some action.

India COVID 19 second wave Mumbai market coronavirus

India response

– Official sources told ANI on November 26 that no case of COVID-19 variant B.1.1.529 has been reported in India so far.

– The Indian SARS-CoV-2 Genomic Consortia INSACOG is closely tracking the new variant of COVID-19 called B.1.1.529 and its presence has not been detected yet in the country, officials have said.

– Government sources have said that India is likely to restrict travellers from South Africa and neighbouring countries as the new COVID-19 variant rises, Redbox India reported.

– Later in the day, the Union Ministry of Health and Family Welfare on November 28 issued new guidelines for international travellers arriving in India, effective December 1. This new set of guidelines has protocols to be complied with international travellers as well those to be followed by airlines, points of entry -- including airports, seaports and land border -- for risk profiling of passengers.

– Among other things, the government also issued a list of 12 countries from where travellers would need to follow additional measures on arrival in India including post-arrival testing.  They include countries in Europe including The United Kingdom, South Africa, Brazil, Bangladesh,  Botswana, China, Mauritius, New Zealand, Zimbabwe, Singapore, Hong Kong and Israel.

– On vaccinations, AIIMS chief Dr Randeep Guleria said the new Omicron variant of coronavirus has reportedly got over 30 mutations in the spike protein region, "and thus the efficacy of vaccines against it needs to be evaluated critically".

– Dr Guleria told PTI: "The new variant of coronavirus reportedly has got more than 30 mutations at the spike protein region and therefore has the potential of developing immunoescape mechanisms. As most vaccines (work by) forming antibodies against the spike protein, so many mutations at the spike protein region may lead to a decreased efficacy of COVID-19 vaccines. The efficacy of vaccines including those in use in India needs to be evaluated critically. The future course of action will depend on what more data on its transmissibility, virulence and immunoescpae shows"

– Union Health Secretary Rajesh Bhushan asked states and UTs to ensure that samples of travellers turning positive are sent to designated genome sequencing laboratories promptly.

– Earlier PTI reported that the Centre, on November 25, asked all states and union territories (UTs) to conduct rigorous screening and testing of all international travellers coming from or transiting through the affected regions – South Africa, Hong Kong and Botswana.

– The contacts of these international travellers are also to be “closely tracked and tested”, as per MoHFW guidelines, Bhushan said.

– Among states, the Delhi government has called a meeting of the Delhi Disaster Management Authority (DDMA) to discuss steps that need to be taken in view of the new threat.

– Chief Minister Arvind Kejriwal said on November 26 tweeted: "In view of the threat from new COVID-19 variant from African countries, we have requested experts to make a presentation to the DDMA on Monday and suggest what steps we should take. We will take all steps necessary to protect you and your family."

Participants, some wearing protective face masks, perform yoga during World Yoga Day in the old quarters of Delhi, India (Image: Reuters/Adnan Abidi)

So, how bad is it?

– Mutations by themselves are not “bad”, they could be inconsequential in terms of vaccines or spread – two loaded factors. The scary part is not knowing everything. But, it does share some mutations with other past variants and this gives scientists some insight.

What is driving concern is that the new strain is so very different from the original SARS-CoV-2 that emerged in Wuhan and this means that vaccines that were developed could potentially fall short.

– There have been many examples of variants that have seemed scary on paper, but had no bad real world impact – case in point: the Beta variant that emerged in South Africa last year and grabbed attention due to its infectivity.

It was however, the Delta variant that spread further and to grim results, having left Alpha, Beta and Mu variants far behind. Of 845,000 sequences uploaded to the GISAID global science initiative with specimens collected in the last 60 days, 99.8 percent were Delta, according to the WHO's weekly epidemiological report.

– In terms of patient experience, a South African doctor who was one of the first to suspect a different coronavirus strain said on Sunday that symptoms of the Omicron variant were so far mild and could be treated at home.

Angelique Coetzee, chair of South African Medical Association, told Reuters that on November 18 she noticed seven patients at her clinic who had symptoms different from the dominant Delta variant, albeit "very mild".

– Although epidemiologists say travel curbs may be too late to stop Omicron from circulating, many countries – including the United States, Brazil, Canada, European Union nations, Australia, Japan, South Korea and Thailand – have announced bans or restrictions on travel from South Africa and other southern African nations.

The South African government has denounced the travel measures as unfair and potentially harmful to its economy, saying it is being punished for its scientific ability to identify coronavirus variants early.

– Also, till date seven SARS-CoV-2 strains that have been labelled “variant of concern” by WHO and ongoing studies and monitoring will give a better picture. This means that not all mutations would be malignant.

– WHO also pointed out that vaccines have reduced transmission of the dominant Delta variant by about 40 percent. By common logic, continuing to vaccinate and maintaining Covid appropriate behaviours such as wearing a facemask, maintaining distance, avoiding crowds and meeting others outside or only in a well-ventilated indoor space, should serve us well.

– As Doctor Faheem Younus (MD) who is VP, CQO and Chief of Infectious Diseases at the University of Maryland UCH, tweeted on November 26: "Afraid of the Nu Variant From South Africa? Know that we don’t know if it’s more lethal, more transmissible or evades immunity. Wait for more facts. Lots of premature conclusions about it & I know fear sells. But public health is a service not a business. Keep calm and carry on" (sic)

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