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INSA COG rotates to take on Omicron

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Having the best whole-genome sequencing infrastructure is only the first step.National adjustments are needed to maximize that potential.

Two years after the SARS-CoV-2 virus gained worldwide attention, just as we thought we were controlling it, another that seems to have more tricks in Corona than its predecessor. The news of the variant has arrived.

Decisions seem to be made in fast forward mode as the world is in pandemic mode. Only two days after South African authorities first reported the variant to WHO, UN agencies designated it as the Fifth Concern (VOC) on November 26, 2021.

Interestingly, on November 30, Dutch health officials revealed a newly named Omicron variant in two test samples taken on November 19 and 23, from a sample from southern Africa. Reported that it occurred a week ago. Therefore, it must be assumed that more than the first two confirmed cases of Omicron from Karnataka already exist in India, and it is only a matter of time before the test appears further.

An important aspect that may prove important in containment strategies is that current SARS-CoV-2 PCR diagnostic kits have multiple mutations in several key areas. It is to keep detecting the body. In the November 26 release of WHO, one widely used PCR test did not detect one of the three target genes (called S gene dropout or S gene target disorder) in some laboratories. It was shown and suggested that this test could be used. Markers for this variant while waiting for sequence confirmation.

Early reports from health authorities in southern Africa show that patients experience “extreme malaise, even with mild illness,” while Omicron variants have so far caused “very low hospitalizations.” However, in an update on November 28, 2021, WHO warned that the first reported infection was in college students (younger individuals who are more prone to milder illness). Therefore, it can take days or weeks to understand the level of severity of the Omicron variant.

“The overall risk associated with Omicron is considered to be very high,” the WHO statement said: “In contrast to previous VOCs, both potential antigenic escape and higher infectivity are serious. It emphasizes “preliminary evidence of Omicrons that may lead to further surges with consequences”.

Strengthening aggressive testing, and more importantly, positive, for India to focus on expanding the scope of the COVID-19 vaccine, fearing that reinfection may be higher. Whole genome sequencing with a high percentage of samples should be included.

With more than 12 labs bearing in mind the criticism that India did not do enough testing or share sequence data with global agencies like GISAID fast enough when the Delta variant rampaged. There are reports that it will be added to 38 existing labs. India SARS-CoV-2 Genomics Consortium (INSACOG) of the Ministry of Health.

If the last two years have been to install bullets (vaccines, drugs, convalescent plasmas, etc.) that fire at enemies, this time we will enhance radar to detect stealth intruders and attempt camouflage and hiding. Overcome.

Therefore, INSACOG, India’s long-standing initiative on “genome sequencing of circulating strains of COVID-19 in India and research and surveillance of viral mutations,” is now an even more important part of anti-COVID weapons.

Fortunately, the pandemic has shortened the overall response timeline. Union Health Minister Rajesh Boushan’s first letter of recommendation to the state on a new variety was November 25, the day before WHO declared it a VOC.

These daily recommendations now need to be translated into effective implementation at the state and district levels. As INSACOG prepares for this latest stress test, having the best infrastructure is only the first step. National adjustments are needed to maximize that potential.

However, Prime Minister Modi himself hinted at this significant gap, and at a briefing on Omicron on November 27, he talked about the need to “increase and expand sequence efforts” and INSAGOG responds better this time. I’m expecting. ..

As of November 30, 2021, Maharashtra accounted for 27.4 percent, Kerala 9.9 percent, and Delhi 8.2 percent of the 70471 genome characterized by INSACOG. However, geographically large states such as Uttar Pradesh contributed 1.5% to INSA COG. This clearly shows that more work needs to be done in the field to solve problems such as supply chain and logistics.

Following Prime Minister Modi’s Nudge, Secretary (Health Research) and DGICMR Dr. Ballam Bhargava inform state health authorities on November 30 that Omicron variants are immune to RT-PCR and rapid antigen testing (RAT). And advised to launch. A test for rapid and early identification of any case.

Manufacturers of RT-PCR and RAT kits such as Thermo Fisher, Abbott, and Mylab ensure that RT-PCR and RAT test kits can detect omicrons even if there are significant mutations in the S gene / peplomer. Similarly, definitive evidence takes at least two weeks, but vaccine makers claim that their injections are still working or are already working on new variants to deal with new variants. I am. This time around, we are searching for variant neutral vaccines and test kits that, at least in theory, offer broader and longer protection.

In fact, Omicron is not the last COVID-19 mutant, even if the fear of antigenic escape leading to its increased infectivity and increased mortality proved to be unfounded. Omicron can explode in a month or in a delta on stage.

But the gift of this pandemic should be, and I am confident, a resilient public health system. This is the only long-standing defense we have to build and participate in. Each adversity has its own lessons. It’s up to us to learn them well.

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INSA COG rotates to take on Omicron

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