“Omicron” Variant, A New Strain of Coronavirus: Check Symptoms, Tests, Impact and Severity

Omicron Variant: What Makes it Undetectable through RT-PCR?

Omicron Variant is classified as a new SARS-CoV-2 variant, identified in South Africa, regarded as a ‘variant of concern’. 

How is this Omicron Variant of Covid-19?

As per the early indications, it is possibly even more transmissible than the highly infectious Delta variant. Hence health experts suggest that current vaccines may be less effective against it.

Mutations that characterize this variant are:

• With 30 mutations in the region that encodes the spike protein, B.1.1.529 has a very unusual constellation of mutations.
• The region with 30 mutations encodes the spike protein, and preliminary analysis suggests that these are responsible for the virus’s entry into human cells. 
• It is highly infectious.

What is the potential impact of the Omicron Variant?

• The phenotypic impact of the mutation is known to affect transmissibility and cause immune evasion. 

Note: Among these mutations already been detected in Delta as well as Alpha variants.

Mutations of concern are:

• As per the research, a cluster of mutations, known as H655Y + N679K + P681H, is associated with more efficient cell entry. Hence, indicating enhanced transmissibility.
• Not only additions but deletions in the mutations are also a cause of concern, and one such is
  sp6, which is similar to a deletion in the Alpha(α), Beta(β), Gamma(γ), and Lambda(δ) variants. 

Note: This may be associated with evasion of innate immunity and could enhance transmissibility and increased effectivity.

The information available on Omicron Variant

• As of now, not much is known as more investigations are underway:

• To determine the possible impact of these mutations on the capacity of the virus to transmit more efficiently
• To impact vaccine effectiveness and evade the immune response, and to cause more severe or milder disease
• In the last two weeks, South Africa has reported a four-fold increase in new cases, coinciding with the emergence of B.1.1.529.

Note: Rapidly increase in the cases was found in the Gauteng province, including Pretoria and Johannesburg. 

• Worldwide, the health authorities need to constantly watch to identify which ones are more important than others. 

• In the last two weeks, South Africa has reported a four-fold increase in new cases, coinciding with the emergence of B.1.1.529.

Note: Rapidly increase in the cases was found in the Gauteng province, which includes Pretoria and Johannesburg.

• Worldwide, the health authorities need to keep a constant watch to identify which ones are more important than others.

How WHO regards Omicron variant?

• This effectively means that Omicron has been demonstrated to be associated with one or more of the following changes: 
  • increase in transmissibility
  • decrease in the effectiveness of diagnostics, vaccines, therapeutics.

Differential Symptoms of Omicron Variant

• No unusual symptoms have been reported so far by the B.1.1.529 variant infection. 
• In fact, as with other infectious variants such as Delta, some individuals are asymptomatic.

Which Tests can be performed to detect Omicron variant infection?

• Tests like Reverse transcription-polymerase chain reaction (RT-PCR) can only confirm whether a person has an infection or not. RT-PCR does not determine which variant has infected the person. To assess and confirm that a genome sequencing study must be done.

Note: Not all infected samples are sent for genome sequencing. The reason is that it is a slow, complicated and costly process. Generally, a very small subset of all positive samples — about 2 to 5 %— is sent for gene analysis.

• When there is a mutation in the spike protein (as with the Omicron variant), then there is a possibility that RT-PCR tests would not recognize the mutation and give a negative result.

Note: The problem is that Omicron is not the only variant with mutations in the spike protein. 

Three prominent aspects of Omicron Variant

a. Good at spreading

• Omicron has around 50 mutations, which potentially make the variant more transmissible. 
• Out of these 50 mutations, 32 are in spike proteins, which the virus uses to enter the human cells, and 10 are mutations of high relevance.

b. Not very severe

• As per some of the experts, the variant will not cause a more severe disease. 
• The new variant may reduce the effectiveness of vaccines, but they will not be rendered ineffective.

c. This indicates that Covid is becoming endemic

• Based on the history of all the infectious diseases, it does happen that viral disease, particularly initially, causes pandemics and over some time they become endemic. 

Note: Endemic means when a disease or infection keeps coming every year but in a milder form. 

Inputs from WHO:

• WHO is coordinating with a large number of researchers around the world to understand Omicron better. 
• Studies currently underway or underway shortly include: –

• assessments of transmissibility,
• the severity of infection (including symptoms), the performance of vaccines and diagnostic tests, and
• effectiveness of treatments

Some of the recommended actions from countries:

• WHO recommends countries to undertake, 

• including enhancing surveillance and sequencing of cases
• Sharing genome sequences on publicly available databases, such as GISAID
• Reporting initial cases or clusters to WHO
• Performing field investigations and laboratory assessments to understand better if Omicron has different transmission or disease characteristics, 
• Impacts effectiveness of vaccines, therapeutics, diagnostics, or public health and social measures.

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