Omicron in community transmission: INSACOG

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Omicron in community transmission: INSACOG
© Provided by Hindustan Times Baramulla, Jan 23 (ANI): A beneficiary receives a dose of the COVID-19 vaccine during a vaccination drive carried out by the healthcare workers with the help of the Indian Army during heavy snowfall, in Baramulla on Sunday. (ANI Photo) (ANI)

The Omicron variant of the coronavirus is now in community transmission in India and has become the dominant strain in multiple major cities, according to the Indian Sars-CoV-2 Genomics Consortium (INSACOG) based on whole genome sequencing results of positive Covid-19 samples.

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The findings by INSACOG are in line with what has been observed by scientists across the world regarding the Omicron variant’s key characteristic of high transmissibility, which enables it to quickly outstrip the circulation of all other variants in any region.

Experts said that this development is not a cause of immediate concern as Omicron is known to cause milder infections compared to other variants such as Delta. This means that it will likely lead to a rapid spike in cases, which cause a far smaller proportion of hospitalisations, and an equally sharp fall in cases – all trends that are already visible in several metros across the country that were the early hot spots of India’s third Covid wave.

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“Omicron is now in community transmission in India and has become dominant in multiple metros, where new cases have been rising exponentially,” read the latest INSACOG bulletin, dated January 10, released on Sunday.

A senior expert from INSACOG, a consortium of 10 central laboratories and 28 regional ones, said that the results were not surprising.

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“This particular variant is known to spread much faster and it would have spread rapidly once it entered into the community. Therefore, the extent of spread is not surprising that way. The silver lining being it does not seem as severe clinically as the Delta variant,” said the expert, who asked not to be named.

The data further shows that while cases continue to rise nationally, cases appear to have already peaked in the major metropolitan areas (the earliest outbreak centres of Omicron variant in India) such as Mumbai, Delhi, Kolkata and Chennai, without leading to any crisis in hospital resources such as beds, medical oxygen, and medication.

In Mumbai, the seven-day average of new cases has dropped more than 67% from the peak of 17,523 cases a day witnessed on January 12. In Delhi, this number has dropped 45% from the January 15 peak of 23,529 cases a day. In Kolkata it has dropped 70%, while it has dropped 10% in Chennai. Most importantly, neither of the cities mentioned above were on the cusp of facing a crisis like they did during the Delta wave. Despite the rapid rise in cases, nearly 80% of beds earmarked for Covid were consistently available through these cities.

Experts said that the Omicron variant is very different from the original virus detected first in Wuhan in 2019, and is far less lethal. “Omicron is a different disease than the original Covid-19; it’s not a killer disease like Covid-19 as show the mortality data. It is a deviant as it has shifted so far antigenically its virulence,” said T Jacob John, former head, virology department, Christian Medical College, Vellore.

“As for national peak, rural areas have to be saturated for that and it has not happened yet. However, cities individually may attain peak, like it happened with Mumbai a few days ago, and is currently happening in Delhi. At most of the other places cases are going up,” he added.

The INSACOG bulletin added that India may not be able to utilise screening for Omicron based on “S-gene dropout”, like many countries have been able to, as a substantial proportion of Omicron infections in India appear to be a lineage (BA.2) that may give higher false negatives in S-gene dropout screening.

“Tests suitable for PCR-based screening applicable to all Omicron lineages have been approved for use,” the researchers from INSACOG said.

The Indian Council of Medical Research (ICMR), the country’s apex biomedical research regulator, has begun approving test kits that it says are capable of detecting all sub-lineages of the heavily mutated Omicron variant. “Among the non-genome sequencing method of detecting Omicron, there is an S-gene target failure which is being used in the UK (TaqPath RT-PCR kits); however, Omicron has three lineages— BA. 1, BA.2, and BA.3, and sub-lineage BA.2 does not cause S-gene dropout and that is 30% of the times and is a problem with the TaqPath kit. Now, an innovative solution has been developed in India which is detecting the S-gene drop-out as well as all three sub-lineages with very high sensitivity and specificity that has been developed by TataMD, and is validated by ICMR,” said Balram Bhargava, director general, ICMR, in one of the recent weekly Covid briefings.

The overall aim of INSACOG has been to monitor the genomic variations in the Sars-CoV-2, the virus that causes Covid-19, on a regular basis through a multi-laboratory network. There are 269 sentinel sites identified across the country from where samples are being collected for testing.

Of the total number of samples sequenced so far, 127,697, sequences have been analysed.

The bulletin also says that the recently reported B.1.640.2 lineage is also being monitored.

The World Health Organization (WHO), in November last year, classified B.1.640.2 as a variant under monitoring.

“There is no evidence of rapid spread and while it has features of immune escape, it is currently not a variant of concern. So far, no case detected in India,” confirmed the INSACOG bulletin.

The rate of hospitalisation during this wave has been much lower compared to the previous wave with Delta, which caused India’s brutal second wave of infections in April-May 2021. The researchers at INSACOG said that due to very high rate of new infections, the absolute number of hospitalisations has crossed previous highs in many countries and is therefore creating stress on health care systems.

However, such a phenomenon of hospitals being overburdened has not yet been observed in India. According to a hospitalisation tracker by HT, which covered 13 regions, more than 85% of Covid beds are currently unoccupied in the country.

While deaths have also been much lower during the new wave, the majority of severe cases and deaths have been seen in unvaccinated subjects or those with severe comorbidities. “The broadest possible protection is going to be through hybrid immunity, which is a result of previous infection plus vaccination,” said Gagandeep Kang, senior vaccine expert, and faculty at Christian Medical College, Vellore.

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