Omicron threat allows private labs to sequence genomes

The government may allow private laboratories to conduct whole-genome sequencing of Sars-Cov-2 positive samples. This is because of the Omicron threat. They will do this to scale up testing facilities in the wake of the threat posed by the heavily mutated Omicron variant. This, the people familiar with the development, said.

There have been talks around it, but no final decision has been made yet on the issue,” a central government official said on condition of anonymity. It was mentioned in the Parliament discussions in the ongoing winter session.

There are 36 laboratories for genome sequencing in the country currently. These laboratories can do whole genome sequencing of up to 30,000 positive samples. Along with it, the capacity is being increased with the help of private laboratories,” health minister Mansukh Mandaviya said last week. He said this while speaking on the Omicron variant during question hour on Friday.

It would make sense to include private labs if the government intends to scale up genetic sequencing to detect mutations early, industry insiders said.

India is performing probably the lowest amount of genetic testing anywhere in the world. We are probably not doing (genome sequencing) of even 1% of the positive samples, whereas there are countries like Israel that are performing genome sequencing of all positive samples.

Even the US is doing it for 20-30% of its positive samples. The next thing is to expand our genetic testing like we did for molecular testing,” said GSK Velu. He is the chairman and managing director of Neuberg Diagnostics. It is one of the country’s largest diagnostic laboratories.

The government should expand the genetic sequencing facility, allowing some of the private labs that have the capacity and capability to perform it.

Genetic testing costs some 10,000 currently, but that can decline to around 5,000 once volumes rise and further fall to as low as 2,000- 3,000 for each test,” Velu said.

Advanced studies are required to determine the amount of drop in the immune response of current Covid-19 vaccines against the new Omicron variant, health experts said.

We absolutely should check and expect to find a significant decline,” said Dr. Gagandeep Kang. He is one of India’s top vaccine experts from Christian Medical College in Vellore, Tamil Nadu.

Messenger RNA (mRNA) vaccines have better NAb (neutralizing antibody) responses than any other class of vaccines, a 40-time decline as shown by Alex Sigal is concerning, though perhaps expected based on the substantial sequence changes,” Sigal.

He is a faculty at the Africa Health Research Institute, on Wednesday tweeted results of experiments on neutralization of Omicron by Pfizer BNT162b2 vaccination elicited immunity.

The variant still uses ACE2 (Angiotensin-Converting Enzyme 2), an enzyme attached to the membrane of cells and used by the virus to enter the host cell, Sigal’s experiments found.

There was a very large drop seen in the neutralization of Omicron threat by the Pfizer vaccine immunity as compared to the parent virus, Sigal found. However, Omicron’s escape from vaccine neutralization is incomplete, suggesting that previous infection plus vaccination still neutralizes.

The National Institute of Virology in Pune, the Indian Council of Medical Research’s apex virology laboratory, is trying to isolate the strain to determine how effective the vaccines that are currently being used in the country are against Omicron, according to people familiar with the matter within the government.

A neutralizing antibody (NAb) is responsible for defending cells from organisms that cause disease. It is produced naturally by the body as part of its immune response, and its production could be triggered by both infection and vaccination against infection.

The Omicron variant is characterized by changes in 30 amino acids (building blocks of proteins), of which 15 are in the receptor-binding domain that connects with the human cells to enter the body, and three small deletions and one small insertion in the spike protein, according to INSACOG, India’s genome testing consortium.

Hybrid immunity for those infected before vaccination may help, but the vaccines were not better against Delta (variant) and so (there is) no reason to assume (they will be) better against Omicron threat.

One may hope, but not assume. Preparation should be based on the decline,” said Anurag Agrawal, director of the Institute of Genomics and Integrative Biology, an institution under the Centre for Scientific and Industrial Research.

The silver lining is that the current vaccines may continue to reduce the risk of death and severe disease, irrespective of the variant. “All vaccines did show effectiveness against severe disease, even with Delta, and that is expected to continue with Omicron threat,” said Agrawal.

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