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Omicron Covid Virus

Omicron – Latest Mutated Form of Coronavirus (Covid-19)

What is Omicron?

Omicron is the latest mutated form of coronavirus (Covid-19) that was first reported to WHO from South Africa on 24 November 2021. It was designated as a variant of concern (VOC) by WHO on the advice of WHO’s Technical Advisory Group known as TAG-VE.

What are different lineages of Omicron?

The Omicron variant comprises four lineages including B.1.1.529, BA.1, BA.2, and BA.3.

What is the Technical Advisory Group on Virus Evolution (TAG-VE)?

The Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE) is an independent group of experts that periodically monitors and evaluates the evolution of SARS-CoV-2 and assesses if specific mutations and combinations of mutations alter the behavior of the virus. The TAG-VE was convened on 26 November 2021 to assess the SARS-CoV-2 variant: B.1.1.529.

Omicron emergence in South Africa

The infections have increased steeply in South Africa in recent weeks, 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.

Why Omicron is a Variant of Concern?

This variant has a large number of mutations, some of which are concerning.

The Omicron variant has 50 mutations overall, with 32 mutations on the spike protein alone. The spike protein which forms protruding knobs on the outside of the SARS-CoV-2 virus helps the virus adhere to cells so that it can gain entry.

It is also the protein that all three vaccines currently available in the U.S. use to induce protective antibodies. For comparison, the delta variant has nine mutations. The larger number of mutations in the Omicron variant may mean that it could be more transmissible and/or better at evading immune protection a prospect that is very concerning.

Omicron is a highly divergent variant with a high number of mutations, including 26-32 in the spike, some of which are of concern and may be associated with immune escape potential and higher transmissibility. The Omicron variant has 10 mutations in the receptor-binding domain the part of the spike protein that interacts with the ACE-2 receptor and mediates entry into cells compared with just two for the delta variant. Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other variants of concern. The number of cases of this variant appears to be increasing in almost all provinces in South Africa.

The Omicron Covid variant has been found to multiply about 70 times quicker than the original and Delta versions of coronavirus in tissue samples taken from the bronchus that could help explain its rapid transmission.

Based on the evidence presented indicative of a detrimental change in COVID-19 epidemiology, the TAG-VE has advised WHO that this variant should be designated as a VOC and the WHO has designated B.1.1.529 as a VOC, named Omicron.

WHO is tracking all variants of Covid-19. A complete list of variants is present here Tracking SARS-CoV-2 variants

Detection of Omicron

Current SARS-CoV-2 RT-PCR diagnostics continue to detect this variant. This method detects specific genes in the virus, such as Spike (S), Enveloped (E), and Nucleocapsid (N) to confirm the presence of the virus.

Several labs have indicated that for one widely used RT-PCR test, one of the three target genes is not detected (called S gene dropout or S gene target failure) and this test can therefore be used as a marker for this variant. Though a minority of publicly-shared sequences lack this deletion, SGTF (S gene target failure) can be used as a proxy marker to screen for Omicron. However, confirmation should be obtained by genomic sequencing, as this deletion can also be found in other VOCs (e.g. Alpha and subsets of Gamma and Delta) circulating at low frequencies globally.

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Using this approach, this variant has been detected at faster rates than previous surges in infection, suggesting that this variant may have a growth advantage.

What countries should do to prevent the outbreak of Omicron?

An outbreak can be prevented or controlled by:

  • enhancing the surveillance and sequencing efforts to better understand circulating SARS-CoV-2 variants.
  • submitting complete genome sequences and associated metadata to a publicly available database, such as GISAID.
  • reporting initial cases/clusters associated with VOC infection to WHO through the IHR mechanism.
  • performing field investigations and laboratory assessments to improve understanding of the potential impacts of the VOC on COVID-19 epidemiology, severity, effectiveness of public health and social measures, diagnostic methods, immune responses, antibody neutralization, or other relevant characteristics.

What people should do to prevent infection from Omicron?

People should take measures to reduce their risk of COVID-19, including proven public health and social measures such as wearing well-fitting masks, hand hygiene, physical distancing, improving the ventilation of indoor spaces, avoiding crowded spaces, and getting vaccinated.

Current knowledge about Omicron 

Researchers in South Africa and around the world are conducting studies to better understand many aspects of Omicron.

Does Omicron have more Transmissibility than other variants of Coronavirus?

Omicron seems to be more transmissible (i.e, more easily spread from person to person) compared to other variants, including Delta.

The Omicron Covid variant has been found to multiply about 70 times quicker than the original and Delta versions of coronavirus in tissue samples taken from the bronchus, the main tubes from the windpipe to the lungs, in laboratory experiments that could help explain its rapid transmission.

What about the Severity of disease caused by Omicron Variant?

 It is not yet clear whether infection with Omicron causes more severe disease compared to infections with other variants, including Delta. Although Preliminary data suggests that there are increasing rates of hospitalization in South Africa, this may be due to increasing overall numbers of people becoming infected rather than just with the Omicron variant.  

The study, by a team from the University of Hong Kong, found that the new variant grew 10 times slower in lung tissue, which the authors said could be an indicator of lower disease severity.

What are the Symptoms of Omicron Variant?

According to Dr. Angelique Coetzee, Chairperson of the South African Medical Association and one of the physicians who first flagged the highly mutated strain in South Africa, Omicron patients experienced severe headache, body pain, tiredness, scratchy throat, and mild fever unlike the common flu-like symptoms of Covid-19.

According to Angelique Coetzee, patients infected with the Omicron variant show extreme tiredness which is not limited to any age group. Young patients also show extreme tiredness, “Although it is yet to be officially listed by the World Health Organisation (WHO).

There is also no major drop in oxygen saturation levels, Coetzee said in media reports. The Omicron patients also reported mild muscle aches, a scratchy throat, and dry cough, according to the doctor. The patients that Coetzee treated were mostly men, aged under 40, and around half of them were even vaccinated. Most patients infected with Omicron strain have recovered without hospitalization.

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Preliminary evidence suggests a potential shift in the tropism of the Omicron variant towards the upper respiratory tract, as compared to Delta and the wild type (WT) virus that has a tropism for the lower respiratory tract.

Effectiveness of prior SARS-CoV-2 infection 

Although the information available is limited, some preliminary evidence suggests there may be an increased risk of reinfection with Omicron. That means the people who have previously had COVID-19 could become reinfected more easily with Omicron, as compared to other variants of concern.

Are Current Covid Vaccines effective against Omicron?

WHO is working with technical partners to understand the potential impact of this variant on existing countermeasures, including vaccines. Vaccines remain critical to reducing severe disease and death, including against the dominant circulating variant, Delta. Current vaccines remain effective against severe disease and death. But as per preliminary data observed by WHO, current covid vaccines may be less effective against infection and transmission of Omicron Variant.

Current evidence consistently shows a reduction in neutralizing titers against Omicron in individuals who have received a primary vaccination series or in those who have had prior SARS-CoV-2 infection. In addition, increased risk of reinfection has been reported by South Africa, the United Kingdom, Denmark, and Israel.

Booster doses may be needed in the future. Although according to WHO, no data is yet available to confirm whether booster doses will be required or will be effective against Omicron.

However, vaccine protection is also by antibodies as well as by cellular immunity, which is expected to be relatively better preserved. Hence vaccines are expected to still offer protection against severe disease and, vaccination with the available vaccines is very important.

Can currently available tests detect Omicron Variant?

 The widely used PCR tests e.g. RT-PCR continue to detect infection, including infection with Omicron.

Most Omicron variant sequences reported include a deletion in the S gene, which can cause an S gene target failure (SGTF) in some PCR assays. As a growing minority of publicly shared sequences (including all BA.2 sublineage sequences) lack this deletion, using SGTF as a proxy marker to screen for Omicron will miss Omicron lineages lacking this deletion.

Are current treatment options avaialble for Coronavirus (Covid-19) effective against Omicron variant?  

Therapeutic interventions for the management of patients with severe or critical COVID-19 associated with the Omicron variant that targets host responses (such as corticosteroids, and interleukin 6 receptor blockers) are expected to remain effective.  However, preliminary data from preprint publications suggest that some of the monoclonal antibodies developed against SARS-CoV-2 may have decreased neutralization against Omicron. Monoclonal antibodies will need to be tested individually for their antigen binding and virus neutralization, and these studies should be prioritized

Other treatment options will be assessed to see if they are still as effective given the changes to parts of the virus in the Omicron variant. 

Current situation of Omicron variant in India:

Currently, there are more than 10000 cases of Omicron in India. As of today, the Omicron variant had been identified in 171 countries across all six WHO Regions.

The United Kingdom reported the first death of a person infected with the new Omicron variant of the coronavirus followed by Isreal and the US.

Will there be a third wave?

Omicron cases are increasingly being reported from countries outside of South Africa and given its characteristics, it is likely to spread to more countries including India. However, the scale and magnitude of the rise in cases and most importantly the severity of the disease that will be caused is still not clear. Further, given the fast pace of vaccination in India and high exposure to delta variant as evidenced by high seropositivity, the severity of the disease is anticipated to be less than the delta variant.

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The Third Wave of Covid cases from Omicron Variant has already started in many countries including India. Many of these countries are now reporting a slow down of cases by omicron as compared to previous weeks.

Weekly Update on SARS-CoV-2 Omicron variant

Omicron has a substantial growth advantage over Delta, and it is rapidly replacing Delta globally. There is now significant evidence that immune evasion contributes to the rapid spread of Omicron, but further research is needed to better understand the relative contribution of intrinsic increased transmissibility and immune evasion in explaining transmission dynamics. While the BA.1 lineage has previously been the most dominant, recent trends from India, South Africa, the United Kingdom, and Denmark suggest that BA.2 is increasing in proportion. Drivers of transmission and other properties of BA.2 are under investigation but remain unclear to date.

The overall risk related to the new variant of concern Omicron remains very high. Consistent evidence shows that the Omicron variant has a growth advantage over the Delta variant with a doubling time of 2-3 days and a rapid increase in the incidence of cases is seen in a number of countries, including those where the variant has become
the dominant SARS-CoV-2 variant, such as the United Kingdom and the United States of America. However, a decline in the incidence of cases has now been observed in South Africa.

The rapid growth rate is likely to be a combination of both immune evasion and intrinsic increased transmissibility of the Omicron variant. Early data from the United
Kingdom, South Africa, and Denmark suggests there is a reduced risk of hospitalization for the Omicron compared to the Delta variant, however, further data are needed to understand the clinical markers of severity including the use of oxygen, mechanical ventilation and death, and how severity may be impacted by vaccination and/or prior SARSCoV-2 infection.

It is also expected that corticosteroids and interleukin 6 receptor blockers will remain effective in the management of patients with severe disease, however, preliminary data suggest that monoclonal antibodies may be less able to neutralize the Omicron variant.

Reassuringly, preliminary data suggests testing using either PCR or antigen-based rapid diagnostic tests (Ag-RDT) assays does not appear to be impacted by the Omicron variant.

Global risk assessment

Based on the currently available evidence, the overall risk related to Omicron remains very high. Omicron has a significant growth advantage over Delta, leading to rapid spread in the community with higher levels of incidence than previously seen in this pandemic. Despite a lower risk of severe disease and death following infection than previous SARS-CoV-2 variants, the very high levels of transmission nevertheless result in a significant increase in hospitalization, continue to pose overwhelming demands on health care systems in most countries, and may lead to significant morbidity, particularly in vulnerable populations.

WHO and MoHFW, GoI