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Maharashtra: Genome sequencing down by 58.6% since May, experts call for stepping up surveillance

Data shows that the total number of genome tests conducted in November in Maharashtra was nearly 58.6 per cent less than that conducted in May. As per the protocol, genome sequencing tests should be conducted on 5 per cent of total samples that have tested positive for Covid-19.

Written by Rupsa Chakraborty | Mumbai |
Updated: December 24, 2021 10:26:56 am
Genomic sequencing gives important information about the type of virus, its mutations, mode of attack and transmissibility.(File)

Even as researchers are racing to detect Omicron, the latest SARS-CoV-2 variant of concern, by sequencing the genomes of coronaviruses infecting people, experts have raised a red flag as genome sequencing in Maharashtra has dropped by 58.6% since May.

Genomic sequencing gives important information about the type of virus, its mutations, mode of attack and transmissibility.

Data shows that the total number of genome tests conducted in November in Maharashtra was nearly 58.6 per cent less than that conducted in May. As per the protocol, genome sequencing tests should be conducted on 5 per cent of total samples that have tested positive for Covid-19.

In April, the state roped in the Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB) to expedite genome sequencing. As per the MOU, the state is supposed to send 3,600 samples every month for genome sequencing, 100 from each district.

“Maharashtra has conducted over 21,000 genome sequencing since the outbreak of the pandemic, the highest in India. We are trying to conduct nearly 4,000 sequencing every month,” said Dr Pradeep Awate, state surveillance officer.

However, the data collected from the public health department shows that with the flattening of the pandemic curve, samples sent for genome sequencing from Maharashtra to CSIR-IGIB dropped by 58.6% from May to November.

In May, 3,515 samples underwent genome sequencing at CSIR-IGIB, and dropped to 3,414 the next month. It decreased further to 2,457 in July, then to 1,862 in August and 1,313 in September. In October, around 1,200 samples were sequenced.

However, with the increase in surveillance due to the discovery of the new variant Omicron, over 1,455 samples were sent to CSIR-IGIB for sequencing in November. The data for December from all the labs are yet to be collaborated.

When The Indian Express spoke to officers in-charge of the laboratories, they attributed it to fewer active Covid-19 cases, which decreased the sample size for genome sequencing.

Since September, the active caseload in the state has decreased by 86%. On September 1, the state had 51,238 active Covid-19 cases, which dropped to 7,350 on December 22. This impacted sample collection for genome sequencing, especially in districts like Nandurbar, Hingoli, Akola and Bhandara, with 2-5 active Covid-19 cases each.

Dr Mahendra Chavan, district health officer, Nandubar said, “Since August, we have been having 4-8 active cases. We have been running random tests on floating populations but there was no directive to send such samples for genome sequence.”

A similar issue was witnessed at the civic-run Kasturba Gandhi Hospital, which was lagging behind in genome sequencing due to inadequate samples. “At least 350 samples are needed to run the genome sequencing. Due to fewer cases, contact tracing was less. This decreased the flow of samples. Also, some samples didn’t meet the requirement of viral load quantity (<25 Ct),” said Suresh Kakani, Additional Commissioner, BMC.

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Experts said that more samples should be sent for genome sequencing even though cases are dropping.

“Due to a similar mistake last year, we took a lot of time to identify Delta variants, which led to a severe outbreak of the virus in the second wave. Low caseload cannot be an excuse,” said Dr T Jacob John, a virologist and retired professor at the Christian Medical College, Vellore.

Dr Prashant Thakare, head of the government molecular diagnostic laboratory in Amravati, said that as Delta is still dominant in the state, it is essential to keep surveillance on its mutations. “We never know how one mutation will behave. So, not only for Omicron, through genome sequencing, we also need to focus on Delta variants,” he said.

In the wake of Omicron, the state has instructed districts to send more samples for genome sequencing. Five labs in Pune that have formed Pune-COG consortium of laboratories have geared up to restart genome sequencing. These include NCCS, National Institute of Virology (NIV), National Chemical Laboratory (NCL), BJ
Medical College and Indian Institutes of Science Education and Research (IISER).

The districts have been instructed to intensify surveillance and send samples of Covid-19 positive international fliers and their close contacts, patients with reinfection, breakthrough infection along with symptomatic abnormality for genome sequencing.

“The state needs to focus on sentinel surveillance as per the World health Organization. Also, take 5% of the samples from patients with upper respiratory tract infection, suspected OPD patients and symptomatic patients for genome sequencing. Along with institutional patients, the state needs to collect samples through house-to-house surveillance,” said Dr Subhas Shalusnke, member of the Covid national task force.

At present, the state has 4,600 monthly capacity for genome sequencing. “We are trying to increase it by starting more genome sequencing labs in Aurangabad and Nashik, which will cost over Rs 15 crore. We have already started working on it,” said Rajesh Tope, state Health Minister.

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