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Covid-19 variants: Comparative analysis of Omicron, Delta, Beta, and other variants, here’s what clinical scientist Muge Cevik’s study suggests

There’s a lot we don’t yet understand about Omicron, including its impact on immunity and what it means for vaccines. Here’s what clinical scientist Muge Cevik has to say about the emerging omicron virus in South Africa.

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Top News Live Updates: India reports 2,58,089 COVID-19 cases, 385 deaths in last 24 hours

By Kritika Bobal

New year, new Covid variant!

Alpha, Beta, Gama, Delta and now Omicron. The Covid-19 variant feels like a loop. It’s been 2 years since the pandemic hit and it doesn’t seem to end anytime soon. The latest Omicron variant was first detected in South Africa and since then it is growing at a rapid pace. Within 10 days it has already spread to more than 36 countries.

There’s a lot we don’t yet understand about Omicron, including its impact on immunity and what it means for vaccines. Here’s what clinical scientist Muge Cevik has to say about the emerging omicron virus in South Africa.

What we might expect & how to interpret the emerging data?

1- Genomic data:
According to Cevik, the biggest concern with omicron is that it contains more than 30 mutations in just the spike protein, the part which helps it enter human cells and the target for vaccines. This mutation profile is very different from other variants of the corona. There are plausible biological consequences of some of these mutations, but we don’t really know the combined effect of all these mutations, so the full significance of omicron is uncertain.

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So where did Omicron come from? And when? When did the lineage branch off? How old is Omicron itself?

For how long Omicron has been circulating is an important question. Most estimate land ~ mid-October & identification of cases with no travel links to SSA indicates early evidence of community transmission.

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According to Immunologist Kristian G. Andersen Andersen, it’s clear that the lineage leading to Omicron is old – possibly mid-2020, but there’s a huge amount of uncertainty in exactly when and where. We also don’t know from what basal lineage this branched off and convergent evolution makes this tricky.

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Adding further Anderson said that, we believe (a) the lineage leading to Omicron branched off a long time ago, (b) Omicron is young, but (c) is already widespread in parts of Africa. So what led to Omicron? Three main hypotheses:

a. Undetected circulation
b. Immunocompromised patient(s)
c. Animal reservoir

2- Epidemiological data:

According to Cevik, epi data could give clues regarding the growth rate. There are several analyses about Gauteng indicating omicron seems to spread quickly, right increasing from ~0.8 to >2. Prelim evidence from South Africa suggests this might be driven by an increased risk of reinfection.

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It’s especially concerning that omicron is increasing not only in Gauteng province but also in other parts of South Africa, which could be an indication that the rapid rise is likely not due to other factors such as behaviour.

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So, putting all these observations together, we can make an assumption that there might be a correlation between omicron and increased rates of infection.

3- Modelling data

Rapid displacement of existing Delta by Omicron in SA is a key clue that it’s likely growing fast, at least in pop with a 25% vax rate & high immunity from prior infection. We don’t really know whether a similar picture will play out in other countries.

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We’ve seen other variants that had us concerned — beta would be the best example. While it had an impact on immune response, it’s been outcompeted w/ intrinsically more transmissible variant, delta. We don’t know the answer as to how this is going to go for omicron.

One of the strongest pieces of evidence to monitor is the trend in other countries, not only increase in omicron cases as this is expected but the replacement of delta. For instance, incidental S-gene target failure (SGTF) seems to be a proxy for omicron due to 69-70del.

Data from England shows a recent uptick in cases w/ SGTF, but this is early data and could indicate importations & linked secondary cases rather than community transmission. So, researchers are carefully watching this data.

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4- Immune response

Mutations in the omicron might mean the immune response generated by vaccination (or prior infection) may not target it as well. Important to remember that immune response provides multilayer protection – it is unlikely that all protection will be lost.

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Muge Cevik also said that when considering vaccine effectiveness against new variants, there are at least three elements to consider.

Read Also: Omicron scare: 5 things to be taken care of before you plan to travel

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India registers 313 new Covid cases, active cases reach 2,041, 3 deaths recorded in last 24 hours

The currently available data suggests that the JN.1 variant is neither leading to an exponential rise in the new cases nor a rise in the hospitalization and mortality.

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India saw a single-day rise of 313 new Covid cases, while the active caseload has declined to 2,041, the health ministry said on Saturday.  Three deaths: two from Karnataka and one from Maharashtra were reported in the last 24 hours.

According to the ministry website, the number of active cases in the country stood at 2,331 on Friday. The number of cases of Covid had dropped to double digits till December 5, but it began to start increasing after the emergence of a new variant and cold weather conditions.

 According to reports after December 5, the highest single day rise of 841new cases was reported on December 31, 2023, which is 0.2% of the peak cases reported in May 2021. Of the total active cases, a large majority of these (around 92%) are recovering under home isolation.

The currently available data suggests that the JN.1 variant is neither leading to an exponential rise in the new cases nor a rise in the hospitalization and mortality. India has witnessed three waves of Covid in the past with its peak incidence of daily new cases and deaths being reported during the delta wave in April June 2021.

 At its peak, 414,188 new cases and 3915 deaths were reported on May 7, 2021. Since the pandemic started in early 2020, there have have been 4.5 crore people who have got infected and this has resulted in the death of 5.3 lakh persons in a total time span of four years.

According to the ministry data, the total number of persons who have recuperated from the disease are 4.4 crore with total recovery rate recorded is 98.81%. A total number of 220.67 crore doses of Covid vaccines have been administered in India so far.  

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India registers 605 new COVID-19 cases and 4 deaths in last 24 hours

The number of people who have recovered from the disease has gone up to 4,44,81,341, an increase of 648 since Sunday morning. In Kerala a 70 year-old male with chronic obstructive pulmonary disease (COPD) and 81year-old male with T2DM and HTN, and in Karnataka, a 48 year old male with CA and TB died, while one person in Tripura succumbed to COVID.

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India recorded 605 fresh COVID-19 cases and four deaths in the last 24 hours. The active cases have increased to 4002, while India’s overall COVID case tally stands at over 4.5 crore (4,50,18,792). The death toll was recorded at 5,33,396 with four new deaths – two from Kerala and one each in Karnataka and Tripura – reported in the last 24 hours, the data updated at 8am stated.

The number of people who have recovered from the disease has gone up to 4,44,81,341, an increase of 648 since Sunday morning. In Kerala a 70 year-old male with chronic obstructive pulmonary disease (COPD) and 81year-old male with T2DM and HTN, and in Karnataka, a 48 year old male with CA and TB died, while one person in Tripura succumbed to COVID.

The Indian Council of Medical Research (ICMR) reported that 11,838 doses of the vaccine had been administered in the country till January 7. The data is a compilation of the Integrated Disease Surveillance Programme (National Centre for Disease Control), media bulletins and websites of various states at 8am on January 4.

As the winter season sets in, health experts are highlighting a sudden surge in viral infections, influenza, and COVID-19 cases. Dr Nikhil Modi, a senior pulmonologist at Indraprastha Apollo Hospital, pointed out that the decrease in temperature leads to increase in moisture in the air, low wind speed and also causes an increase in pollution levels. This contributes highly to various infections.

Due to the decrease in temperature the fog combines with the pollution in the air which further leads to the formation of smog. This condition of the atmosphere can cause different types of infections and difficulty in breathing. Both the state and the central government are keeping a close watch on the new Omicron Subvariant JN.1. J.N.1 is a Variant of Interest (VOI) which is under intense scientific scrutiny.   

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India records 774 new Covid-19 cases, 2 deaths in 24 hours

The number of daily cases was in double digits till December 5 but it started to rise again amid cold weather conditions and after the emergence of new Covid-19 variant, JN.1.

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India on Saturday had a single-day rise of 774 Covid cases while the number of active cases stood at 4,187, the Union health ministry said. As many as two deaths – one each from Tamil Nadu and Gujarat were reported in a span of 24 hours. Of the 4,187 active cases, the majority (over 92%) are recovering under home isolation.

The number of daily cases was in double digits till December 5 but it started to rise again amid cold weather conditions and after the emergence of new Covid-19 variant, JN.1. The central government has asked the state government and union territories to maintain a constant vigil amid an upward trend in the number of Covid-cases and the detection of the JN.1 sub variant in the country.

According to reports after December 5, the highest single-day rise of 841 cases was reported on December 31, 2023, which was 0.2% of the peak cases reported in May 2021. A health official said that the JN.1 variant is neither leading to an exponential rise in new cases nor a surge in hospitalisation and mortality in the country.

The Karnataka government has made the Covid test mandatory for those with Influenza like illness (ILI) or Severe Acute Respiratory Illness (SARI). Karnataka Health Minister Dinesh Gundu Rao said more than 7000 tests are being done every day and the COVID positivity rate is 3.82%. The positivity rate in the state has not come down yet.

He said those with symptoms are being monitored and tested. Those who are in isolation at home have been told to take extra care. He added it is expected that the trend of decreasing Covid cases may start next week in Karnataka. India has witnessed three waves of Covid-19 in the past with the peak incidence of daily cases and deaths being reported during the Delta wave during April-June 2021. At its peak 4,14,188 cases and 3915 deaths were reported on May 7, 2021.

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