Third Wave – In the absence of confirmed reports on Omicron cases in Rajasthan, what variant are we dealing with here?

Third Wave – In the absence of confirmed reports on Omicron cases in Rajasthan, what variant are we dealing with here?

In Udaipur the number of positive cases shot up by 45X in less than 7 days while reported Omicron count has remained stable at 6 since 24 December. There is no sync in the confirmed Omicron cases count given by State and Central Health departments. There are  valid reasons to believe that we are dealing with  the Omicron variant, though.
Omicron Delta Cases in Rajasthan Udaipur
  • 1,280 persons per lakh have been diagnosed with COVID in Rajasthan
  • Currently 9 districts Rajasthan have a Positivity Rate of more than 10% (Udaipur is 15.3%)
  • Currently 7 districts in Rajasthan have a Positivity Rate of between 5%-10%

The last reported case in Udaipur for the Omicron COVID19 variant was on 4 January. These samples were taken on 24 and 25 December. Hence a gap of 10 days before the government genome sequencing labs confirm the sample to be Omicron or otherwise. As of 25 December, the day to which the last recorded Omicron samples belonged, Udaipur had reported 61 positive cases since the third wave began in November. As of 4 January, Udaipur has recorded 6 Omicron patients, with no additional numbers reported for Udaipur. The two reasons for this could be that there actually are no Omicron variant samples found since then (highly unlikely with the 10% Omicron count) OR the samples have not been sent for testing at the approved laboratories. Why the latter seems likely, is what this post is all about.

On 31 December, the National Centres for Disease Control (NCDC), which are the Union Health Ministry laboratory and the key genome sequencing network for India had asked the states to temporarily suspend sending samples for genome sequencing, since the volume of COVID positive cases had risen tremendously. In Udaipur itself, for eg. the number of positive cases shot up by 45X in less than 7 days. The number of positive cases on 4 January was 9, with a positivity rate of 0.55% and on 11 January, Udaipur took stock of 403 positive cases with a positivity rate of 15.34%. The average daily sampling in the last week was 2,390 while for the week before it was 1,600.

Keeping in view the surge in number of COVID-19 cases and increased flow of samples for next generation sequencing (genome sequencing) to NCDC has resulted in a situation wherein they (NCDC) are not in a position to accommodate samples further (for the time being). ... All labs are requested to store all positive samples as per established protocol till further directions. However positive samples of individuals arriving at IGI Airport (New Delhi international airport) with a history of travel to country of concern/their contacts will continue to be sent to NCDC for sequencing.” - NCDC

As these number shoot up across the country, the NCDC hub that coordinates across 28 laboratories across the country (INSACOG network) are overwhelmed with the mammoth task of genome sequencing for all these samples, hence the directives to cease sending samples to the government laboratories.

Dr. Jaiprakash Muliyil, Chairperson of the Scientific Advisory Committee of NIE at ICMR has claimed that the actual cases with Omicron variant may be upto 90 times more than the reported data, which goes true based on the above situation.

We have learned to live with it, as even during the second wave caused by the Delta variant they always multiplied the number of cases picked up by about 30 to get the real number. After the Delta wave, the surge is Omicron all the way whether you do the testing or confirm it, here's no need for confirmation” – Dr. Jaiprakash Muliyil

India recorded 1,94,720 fresh cases till today morning and 442 deaths in the last 24 hours. While the active cases reached 9,55,319 with a positivity rate of 11.05%, the number of positive cases in Udaipur reached 1,669, with a positivity rate of 15.34%. One Omicron death in Udaipur was confirmed by the Central Health department, marking it the first death due to Omicron in India (73 year old patient who had no travel history and was tested on 15 December, confirmed with Omicron on 25 Dec and died on 31 Dec). As per the official number provided by the Centre, the number of Omicron patients in Rajasthan is 645, which makes it the state with the second highest Omicron patients in India, after Maharashtra, which recorded 1,281 Omicron cases till date. No official reports have been issued by the State Health Department, though media reports have been citing that the Rajasthan state health department has confirmed nearly 28,000 Omicron patients!

We seem to be dealing with Omicron all the way.

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