COVID-19: Omicron vs. Delta

January 14,2022
5 Min Read

Omicron vs Delta

	Omicron	Delta
First detected	Botswana in November 2021.	India in December 2020.
Lineage	B.1.1.529 (3 sub-lineages identified are BA.1, BA.2, and BA.3.)	B.1.617.2
Mutations	Carries 50 mutations not seen in combination before (30+ mutations in the spike protein gene). Several of the spike protein mutations are thought to make it more infectious.	Emerged with more than a dozen mutations – initially called double mutant because of 2 prominent mutations: L452R and E484Q.
Transmissibility	Higher transmissibility compared to Delta (maybe up to 4.5 times more).	Higher transmissibility compared to previous variants.
Severity	Less severe as compared to Delta and Delta plus with fewer hospitalizations seen thus far. This may be due to lesser invasion of the lungs as compared to the upper airways as seen in animal studies.	More severe and possibly, higher mortality as seen in the previous wave last year with a high number of hospitalizations.
S-gene drop-out on RT-PCR*	Seen in many cases of Omicron.	Typically not seen in cases of Delta.
Symptoms	Symptoms overlap considerably and the distinction between the variants CANNOT be made based on symptoms alone.
Symptoms	Asymptomatic to mild in the majority of cases (though moderate to severe cases may be seen). Loss of taste and smell is not a prominent symptom. Night sweats have been more in those with Omicron. Patients report a scratchy throat more than a sore throat. Breathlessness is less common in Omicron.	Symptoms are moderate to severe in comparison. Loss of taste and smell is a prominent symptom. Night sweats are not commonly seen. Sore throat is a very common symptom. Breathlessness is more common in Delta.
Vaccine efficacy	According to the WHO, Omicron causes a reduction in vaccine efficacy against infection and transmission. The Covaxin vaccine booster is also supposedly effective against Omicron.	Most vaccines provide protection against Delta.

*What is the S-gene drop-out?

Certain mutations (del 69-70) in the Omicron variant have caused what’s known as the S-gene drop-out or S-gene target failure (SGTF) when doing the RT-PCR test. What this means is that in RT-PCR tests which target the S-gene of the COVID-19 virus, the S-gene is not detected despite the virus being present (provided the S-gene probe targets the mutated segment). Hence, caution is required when selecting the S-gene as a target for PCR testing, due to the SGTF effect.

*Can S-gene drop-out be used to identify the Omicron variant?

SGTF is possible in the Alpha variant and the Delta variant as well. However, since the Alpha variant is not prevalent and only very few cases of both the Alpha and Delta variants have shown SGTF, the strategy can be very well used for screening for the Omicron variant (though sequencing is the only definitive way).

Also, the Omicron variant has subtypes viz BA.1, BA.2, and BA.3 (so far the BA.3 subtype has yet to be detected in India). Of these three, only BA.1 and BA.3 have the del 69-70 mutation which causes the SGTF. So, an infection with the BA.2 subtype of the Omicron variant will not show SGTF.

In summation, sequencing is the definitive way to identify the Omicron variant. There are, however, some kits coming to market which can specifically detect the Omicron variant eg: Omisure from Tata Medical and Diagnostics.

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