Lack of genome sequencing capacity hampers India’s efforts to track the spread of Omicron

On Monday, Delhi Chief Minister Arvind Kejriwal said all samples testing positive for Covid-19 will now be genome sequenced to detect and isolate the Omicron variant.

Kejriwal’s announcement came two weeks after Union health secretary Rajesh Bhushan wrote to all states directing them to do exactly the same. In his letter dated December 3, Bhushan said, “Samples of all those who test positive must be sent for whole genome sequencing expeditiously” to the laboratories under the Indian SARS-CoV-2 Genomics Consortium, or the Insacog network.

But based on conversations with several state officials, Scroll.in found that states have not followed this advisory.

Dr Rajesh Pandey, a scientist at the Council Of Scientific And Industrial Research-Institute of Genomics and Integrative Biology, which maintains all Insacog data, said, “Ideally at this point sequencing all positive samples will give a clear picture” of Omicron spread.

Genome sequencing studies the genetic makeup of the virus and helps detect mutations and variants that can be of concern.

Omicron was first reported in November by South Africa where it has already become the dominant variant, genome sequencing data from the country shows. A month since, the variant has been reported in 106 countries.

In the United States, the Centers for Disease Control and Prevention on Monday said Omicron was detected in 73.2% sequenced samples, effectively replacing Delta as the dominant variant. Until a week ago, Omicron accounted for 12.6% and Delta 87% of sequenced samples in the country.

Also read: The S-gene test makes it easier to screen Omicron cases. Are labs in India using it?

Rising number of samples sequenced

The World Health Organisation on November 26 had announced Omicron as a “variant of concern”. India has improved its sequencing numbers since then to track the variant, shows weekly data from Insacog, a consortium of 38 laboratories in the country. But data for the samples sequenced in India, although increasing every week, remains low.

India has sequenced 1.26 lakh Covid-19 samples till December 4.

A weekly bulletin of the genome sequencing consortium shows 1,489 samples were sequenced in the November 15-22 week. Considering the over 73,000 cases detected in that week, India sequenced a representative 2.03% of its Covid-19 infections. This rose to 2,136 samples between November 22-29, the same week the World Health Organisation labelled Omicron a “variant of concern”. Sequencing accounted for approximately 3.4% of the Covid-19 cases detected in India that week.

The number of samples sequenced the week after further increased to 4,480 between November 29-December 4, accounting for 8.6% of cases. Data for samples sequenced after December 4 is yet to be shared by the consortium.

Data from the Global Initiative on Sharing Avian Influenza Data, or GSAID, where all countries post their genome sequencing data, shows European countries undertake a high rate of sequencing. Iceland leads with more than 50% of its positive samples sequenced, Denmark over 46% and the United Kingdom over 12%.

In India, laboratories attached with the genome sequencing consortium have not found a worrying number of Omicron infections in the samples sequenced from October and November, indicating that the variant may not have penetrated the country on a large scale during those months. Scientists at these laboratories said they do not believe Omicron has entered the community transmission phase in India yet, adding that the sequencing data mostly found the variant restricted to international passengers who are immediately isolated upon testing positive after landing.

But they also admitted that most of the samples sequenced presently are also those of international travellers.

Focus still narrow

Experts believe that detecting the Omicron variant in the community would require casting a wider net for sequencing. Though the government has expanded criteria for sequencing, they are still narrow.

Dr Himanshu Chauhan, from the National Centre for Disease Control which is coordinating sequencing between the consortium and the states, maintained that the government’s focus on whole genome sequencing remains scientific, first on international passengers from high-risk countries and then reinfection or breakthrough infection cases. “Even the December 3 notification meant to sequence all samples of international passengers who tested positive,” he said.

At a press briefing on December 17, Niti Aayog member Dr VK Paul said it is not possible to sequence all Covid-19 positive samples. “Sequencing is always on representative samples. These are very sophisticated tests and not done in routine laboratories. But we assure you that sufficient, systematic sampling is being undertaken,” Paul said.

Lav Agarwal, joint secretary in the ministry of health and family welfare, said the sentinel laboratories under the consortium have been given targets for sequencing, which has been intensified across India. “It is an epidemiological tool to understand the spread (of Omicron). It is not meant for everyone,” he said during the December 17 briefing.

So far, India has found over 214 Omicron cases. Agarwal said most cases have an international travel history link and cause mild illness or are asymptomatic.

Initially, the focus of sequencing was on travellers from high-risk countries. Since 106 countries have now detected Omicron, the sample sequencing of any person who is positive and has an international travel history is being undertaken. Additionally, reinfections, breakthrough cases, those showing unusual symptoms, or are close contacts of international travellers are also being targeted for sequencing.

Once a laboratory detects a Covid-19 positive sample of any international passenger or a suspected Omicron sample, it reports it to the Integrated Disease Surveillance Programme, which directs it to send the sample to the genome sequencing consortium. Each laboratory under the consortium has been given a geographical jurisdiction to collect and sequence samples. The National Centre for Disease Control monitors the sequencing process.

India is recording 7,000-8,000 fresh cases of Covid-19 daily, of which 40% are from Kerala and 12% from Maharashtra. Delhi is recording over 100 Covid-19 cases per day.

Dr Pandey, of the Institute of Genomics and Integrative Biology, which receives 25-30 positive samples of international passengers every day from New Delhi, said the national capital’s daily caseload is low and therefore sequencing all samples is not a herculean task.

“But Kerala and Maharashtra account for more than 50% of the country’s caseload. It is logistically not possible to sequence all their samples,” he said.

While these states are doing representative sequencing, “in other states, we are doing as much sequencing as possible,” Pandey added. The Institute of Genomics and Integrative Biology receives samples from north India, including Haryana, Delhi and Uttar Pradesh.

Tracking when the variant entered India

Laboratories under the consortium are trying to sequence all Covid-19 positive samples they have from the months of November and October to see if the Omicron variant entered the country much earlier.

Dr Rajesh Karyakarte, head of microbiology department at BJ Medical College, Pune, which is a part of the consortium, said Omicron was not detected in any of the 1,445 Covid-19 positive samples from the last two months sequenced at six laboratories. “We sequenced all Covid positive samples from October and November to understand if the variant sneaked in earlier. But almost all our samples were Delta or its sub-lineages. It continues to be the dominant variant,” he said.

In Mumbai, additional municipal commissioner Suresh Kakani, said they began sequencing samples of all international travellers who tested Covid-19 positive after November 1. So far, 10,394 travellers have arrived from high-risk countries, and 65 have tested Covid-19 positive. “Out of all the samples we sequenced from November, a man who had returned from London was detected with Omicron. He was a frequent flier. He had infected another close contact. Testing of all other contacts came negative. But his sample showed Omicron entered Mumbai in November itself,” Kakani said.

Officials from the consortium laboratories said sequencing all samples that tested Covid-19 positive in October and November is difficult as the laboratories cannot store the lakhs of samples that they test. A tube, smaller than a test tube, can store 80-90 samples of viral RNA at a temperature of -20 to -80 degrees celsius. Most private and public labs have limited storage capacity.

This reporting was supported by a grant from the Thakur Family Foundation. Thakur Family Foundation has not exercised any editorial control over the contents of this article.