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Covid-19: CSIR-IGIB to study 4,000 Maharashtra samples for genome sequencing

The Maharashtra government has roped in the Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB) for genome sequencing of 4,000 samples of Covid-positive patients
By Faisal Malik, Mumbai
UPDATED ON APR 28, 2021 12:33 AM IST

The Maharashtra government has roped in the Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB) for genome sequencing of 4,000 samples of Covid-positive patients. The premier biological research institute of the country will not only sequence the genome and list the number of variants, but will also map behavioural patterns of each strain based on the health issues faced by the patients and the treatment provided.

Genome sequencing is an exercise to study changes in the structure of the virus over time. A combination of changes in the ribonucleic acid of the virus can give birth to a new variant. CSIR-IGIB will collect 100 samples from each district and send them to the National Centre for Cell Science (NCCS), Pune and CSIR-IGIB, Faridabad for genome sequencing. It will start in 10 districts, where samples will be collected for a month (100 samples from each district), followed by another 10 districts the next month. This will go on until all 36 districts in the state are covered. The study will be completed in four months, officials said. The aim is to help the state identify the number of active strains in Maharashtra, their effect on human bodies and determine the change in treatment protocol or public health strategies required to contain the spread, officials said.

Chief secretary Sitaram Kunte confirmed that a memorandum of understanding has been signed between the state medical education department and CSIR-IGIB to start the project. “CSIR-IGIB will collect around 100 samples from each of the districts. It will also take clinical data of the treatment prescribed to each patient and their response to the treatment. The research organization will list the number of variants found during the genome sequencing process and also map their patterns that include how they affected the human body or which part of the body, etc. It will also help ascertain if there are different variants infecting citizens in different regions of the state,” Kunte said.

Among the worst-hit states, Maharashtra is yet unaware of the number of strains and their behaviour that may have led to the surge in cases. The National Centre for Disease Control (NCDC) recently confirmed the presence of a double mutant variant in the tested samples, but also said the data was not enough to attribute the surge to it, officials said. “The double mutant variant has been found in 206 samples in Maharashtra. It is high in Nagpur, at 20% of the samples, but there is not enough data to correlate it with the nature of the surge,” NCDC said on April 14.

At 24%, the double mutation virus – now classified as B.1.617 – was the most common in the samples sequenced in the 60 days prior to April 2. The variant was first detected on October 5 and was relatively obscure till it was found in increasing number of samples from January, the India situation report on showed. On April 1, it accounted for 80% of all analysed genome sequences of mutant variants sent by India to the global repository GISAID. B.1.617 was first found in a large number of samples in Maharashtra, the first hot spot of the second wave of infections, which, till April 7, added more than half the new cases being recorded in the country.

Maharashtra has so far reported around 4,400,000 cases and average daily cases have been around 59,000 a day this month. It has also reported maximum casualties and the tally has reached around 66,000.

Dr Shashank Joshi, who is handling responsibility for coordination of the project, said they know there are variants of concern, but to correlate this we have to match the clinical data such as symptoms, age etc. with the genetic data. “We need to collect more data to say the current variants of concern are responsible for the current circumstances. We will be collecting district-wise random samples every week in a systematic way. These samples will be sent to the NCCS, Pune laboratory and IGIB laboratory, Faridabad and then the data will be used to determine district-wise strategies,” Dr Joshi, who is also a member of a state appointed task force for the clinical management of critical patients, said.

Currently, 13-14 districts in Maharashtra are badly hit with the pandemic. “They are now in the phase of recovery, but there are variants of concern operating in each district. This independent survey will give us a deep understanding of what is happening. It will also give us insights on our public health strategies or treatment strategies whether they need to be modified,” he clarified.

Dr Anurag Agrawal, director, CSIR-IGIB, said he would comment only after commencement of the project.

Saurabh Vijay, secretary of state’s medical education department, said the study is necessary to take necessary steps in advance. “It is natural behavior of the virus to mutate. In such a scenario, we need to understand at least what is happening with the changing behaviour of the virus so that we can be better prepared,” he said.

The ministry of health and family welfare, in its statement issued on March 24, said that 771 of the 10,787 samples that were sequenced were found to have the variants of concern (VOC). The Centre last month said that three known VOCs were also found in Maharashtra. The Centre revealed 56 of these were B.1.1.7, five B.1.351 and one P.1.

State health minister Rajesh Tope recently said 1,100 samples have been collected from Maharashtra as part of regular surveillance of genome variations and of them, 500 samples have been examined. “We have sought a detailed report from the Centre, but were informed that it will be made available only at the end of the research,” Tope said to a news daily???

In another release issued on April 16, the ministry also said the states were advised to send samples of genome sequencing along with clinical data of positive patients, but many states are not doing so. A consortium of 10 national laboratories called — Indian SARS-CoV-2 Consortium on Genomics (INSACOG) — was formed in December 2020 to carry out genome sequencing of circulating viruses and correlate the findings with other trends. “The INSACOG guidelines were shared with states. It would have helped INSACOG discover other variants of concern. However, several states, including Maharashtra, Madhya Pradesh, Rajasthan and Kerala have not shared such data, although others, including Punjab and Delhi have,” it stated.

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