Everything You Need To Know About Omicron

Everything You Need To Know About Omicron

Only a week has passed since Botswana and South African scientists made the world aware of the rapidly expanding variant of SARSCoV2, now known as Omicron.

Researchers around the world are striving to understand the threat this variant (currently identified in more than 20 countries) poses to the world.

However, it can take weeks for scientists to draw a more complete picture of Omicron and understand its infectivity and severity, as well as the possibility of bypassing the vaccine and causing reinfection.

Molecular microbiologist Senjuti, director of the Child Health Research Foundation in Dhaka, Bangladesh, says:  ”  Everywhere we go, we are asked about Omicron. Scientists, too, have little understanding of what is happening. ”   

 Nature summarizes what scientists have ever known about  Omicron variants.

How fast does Omicron spread?


The rapid rise in Omicron in South Africa is of greatest concern to researchers, as it suggests that this variant can cause an explosive surge of 19 COVID cases elsewhere.

 On December 1, South Africa recorded hundreds of 8,561 cases per day from 3,402 on November 26 to mid-November, with much of the growth taking place in Johannesburg’s hometown of Gauteng. .. Epidemiologists measure epidemic increases in R. This is the average number of new cases caused by each infection.

R is above 2 in Gauteng, an infection discovered by the National Institute for Infectious Diseases (NICD) in Johannesburg in late November.

A doctor who specializes in infectious diseases at the University of KwaZulu Natal in Durban, South Africa, said at a press conference last week that the increase was last seen early in the pandemic.

Evolutionary biologist Tom Wenselias of the Catholic University suggested that Houten’s R-value was well below 1 in September, suggesting that Delta was the predominant mutant and the number of cases was reduced. .. Of Belgium’s Ruben.

Based on the proliferation of 19 COVID cases and sequence data, Wenserias estimates that Omicron can infect 3 to 6 times more people than Delta over the same period.  ”  The benefit to viruses is greater than the benefit to us,  ”   he adds.

Researchers will observe how Omicron spreads in other parts of South Africa and around the world and better assess its relocation potential, Christian Althaus, a computer epidemiologist at the University of Bern, Switzerland.

House says. With increased surveillance in South Africa, researchers may overestimate Omicron’s rapid growth.    

 Althaus says that, if this pattern repeats itself in other countries, it would be very convincing evidence that Omicron has a transmission benefit.

If it does not occur in European countries, the situation might be a bit more complicated and highly dependent on the immunological situation, so we need to wait. ”   

 Genome sequencing is required to identify Omicron cases, but some PCR tests can detect variant features that distinguish them from deltas.

Based on this signal, there are early signs that the number of cases is increasing, although very few in the UK.  ”  That’s certainly not what we want to see right now, and it suggests that Omicron may certainly have a transmission advantage in the UK as well, ”   Altohaus adds. 


Can Omicron overcome immunity to vaccines and infectious diseases?

The rapid increase in this subspecies in South Africa suggests its ability to evade immunity. About a quarter of South Africans are fully vaccinated, and Wenseleers said that the majority of the population is likely to have been infected with SARSCoV2 in previous waves,  based on the increase in mortality since the onset of the pandemic.

Says. In this regard, Omicron’s success in southern Africa may be primarily due to its ability to infect those who have recovered from COVID 19 caused by Delta and other variants, and those who have been vaccinated. .. Preprint 1 by NICD researchers on December 2 showed that reinfection in South Africa increased with the spread of Omicron. The ideal environment for the creation of Immunscape variants is, unfortunately, this one, ”  says Althaus.

How well the mutant spreads elsewhere can depend on factors such as vaccination and previous infection rates, said Aris Katzourakis, who studies viral evolution at Oxford University in the United Kingdom. increase.  ”  Mixing it with a mass vaccinated population that has given up on other control measures can be ahead of the curve. ”   

Researchers hope to determine how well Omicron evades immune responses and what protection they provide. For example, a team led by NICD virologists Penny Moore and the University of the Witwatersrand in Johannesburg have applied Omicron to neutralize antibodies or have been caused by previous infections or vaccinations to prevent cell infections. It measures your ability to block viruses. To test this in the lab, her team creates  ”  pseudovirus ”   particles.

 This is an engineering version of HIV that infects cells using the SARSCoV2 spike protein, as well as Omicron, which contains up to 32 spike changes. Another South African team, led by Alex Sigal, a virologist at the Africa Health Research Institute in Durban, is using infectious SARSCoV2 particles to perform similar tests on virus-neutralizing antibodies.


Including a team led by virologist Pei Yong Shi at the University of Texas at Galveston, we are working with manufacturers of Pfizer BioNTech vaccines to find out how they can tolerate Omicron. When he saw the constellation of mutations at the top, he was really concerned.  ” We need to wait until we know what the results are. ”  

Previous studies of Omicron spike mutations, especially in the region that recognizes receptors on human cells, suggest that mutants reduce the effectiveness of neutralizing antibodies. For example, in Nature Paper 2 in September 2021, a team led by Paul Bieniasz, a virologist at Rockefeller University in New York City, developed a strongly mutated version of Spike, a virus that cannot cause COVID 19. With Omicron.  ”  Polymutant spikes ”   were found to be completely resistant to neutralizing antibodies in most people  who  received two mRNA vaccines or were tested to recover from COVID 19. At Omicron,  ”  I’m hoping for a solid hit, ”   says Vienius.

 How does the vaccine against Omicron work?

Although Omicron can evade neutralizing antibodies, this does not imply that immunity induced by vaccination and previous infections is not effective in protecting the mutant.

Miles Davenport, an immunoscientist at the University of New South Wales in Sydney, Australia, suggests that immunological studies can protect people from severe forms of COVID 19 with moderate amounts of neutralizing antibodies. Other aspects of the immune system, especially T cells, are less susceptible to Omicron mutations thanantibody reactions. Researchers in South Africa are planning to measure the activity of another immune factor called T cells and natural killer cells.

 This can be particularly important in protecting against severe COVID 19, says Shabir Madhi, a vaccination scholar at the University of the Witwatersrand. Maddy, who has led the COVID19 vaccine research in South Africa, is also part of an effort to conduct epidemiological research on the efficacy of the vaccine against Omicron. There are individual reports of breakthrough infections with all three vaccines administered in South Africa (Johnson & Johnson, Pfizer-BioNTech, Oxford-AstraZeneca). However, Maddy says researchers want to quantify the level of protection against vaccines and Omicron from previous infections.


 He believes the results are reminiscent of the effects of the AstraZeneca-Oxford vaccine on the beta variant, an immune defence variant identified in South Africa in late 2020, but the actual analysis in Canada is from hospitalization. Showed more than 80% protection. If Omicron did the same, Maddy says.

There are many breakthrough infections and many reinfections. However, community case rates are out of control compared to hospitalization rates. According to early reports, most breakthrough infections with Omicron were mild, says Maddy. My interpretation of this is that it is a positive signal. “

 Do current boosters improve protection against Omicron?

Due to the threat of Omicron, some rich countries like the United Kingdom are accelerating and expanding the adoption of booster immunization for COVID vaccines. However, it is not yet clear how effective these doses are against this variant. A third dose increases neutralizing antibody levels, which is likely a breakwater against Omicron’s ability to bypass these antibodies, says Vienius.

His team’s study of polymutant spikes found that people who recovered from COVID 19 months before vaccination had antibodies that could block mutant spikes. In the case of  Bieniasz, these results suggest that people who are repeatedly exposed to SARSCoV2 peplomers are  ”  very likely to have a neutralizing effect on Omicron, ”   whether by infection or booster immunity. Though we are not sure about it.

Does Omicron cause milder or more severe illness than previous variants?

 Early reports raised the expectation that Omicron was associated with a mild illness, and that the variant could be less severe than some of its predecessors. However, these reports (often based on anecdotes and sparse fragments of data) can be misleading, warns Mücke Çevik, an infectious disease specialist at the University of St Andrews, UK.  ”  Everyone is trying to find data that can guide us, ”   she says.  ”  However, at this point, the task is very difficult. ”  

 The main challenge in assessing the severity of a subspecies is to control many confounding variables that can affect disease progression, especially if the outbreak is geographically localized. For example, reports of mild illness due to Omicron infection in South Africa may reflect the fact that South Africa’s population is relatively young, many of which are already exposed to SARSCoV2.


Early in the delta outbreak, it was reported that this subspecies caused more serious illness in children than in other subspecies. This is a collapsing association as more data is collected, says Çevik. Scientists will examine data from other countries about Omicron infections.

This geographical distribution and the larger sample size associated with the increase in cases gives researchers a better idea of ​​how generalized early reports of mild illness can be. Ultimately, researchers want to conduct a case-control study in which two groups of participants are coordinated with each other in terms of key factors such as age, vaccination status, and health status.

The number of hospitalizations can be affected by the total capacity of the hospitals in the area, so data for both groups should be collected at the same time. Most importantly, researchers need to control the degree of economic deprivation. Rapidly expanding new variants may reach groups at risk due to their working or living conditions more quickly, says Çevik. And such groups often suffer from more serious illnesses.

This all takes time.  ”  I think the severity question will be one of the last things we can solve, ”   she says.  ”  That’s what happened to Delta. ”  

 Where is Omicron and how are scientists tracking it?

While more and more countries are aware of Omicron variants, their ability to rapidly sequence the virus from the positive COVID 19 test is focused on wealthy countries. That is, the initial data on the diffusion of Omicron is distorted. Surveillance efforts in Brazil and several other countries leverage clear results from specific PCR tests and can find potential Omicron cases for sequencing, Brazil. According to Renato Santana, a virologist  at the Federal University of Minas Gerais.

This test looks for segments of three viral genes. One of them is the gene that encodes the spike protein. Mutations in the Omicron spike gene prevent it from being detected in the test. That is, a sample containing a variant will test positive for only two genes. Still, not everyone uses this test, and it can take some time to fully map the spread of Omicron. Anderson Brito, a computer virus scientist at the All for Health Institute in Sao Paulo, Brazil, says that few can afford it, despite the guidelines requiring the country to sequence 5% of samples that test positive for SARSCoV2.


Is called Brito fears that travel bans imposed on South Africa and other South African countries following the discovery of  Omicron could discourage governments from disclosing genomic surveillance data.  ”  We punish those who do a good job, ”   he says.  In Bangladesh, which has sequenced about 0.2% of positive coronavirus samples, researchers are working to speed up the sequencing and monitor Omicron and other new variants, Saha said. However, resources are limited. She added that Bangladesh is recovering from a massive dengue outbreak.  ”  In the Global North and Global South, we are all worried about COVID, but let’s not forget our endemic, ”   Saha says.  ”  There are many things we can do. ”  

edited and proofread by nikita sharma

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