Researchers and microbiologists believe that India has sufficient infrastructure for an efficient surveillance system.

New Delhi: With India reporting two cases of Omicron, researchers and microbiologists in the country strongly believe that India has sufficient infrastructure for an efficient surveillance system. Currently, many researchers in India believe that India is quite efficient in terms of genome sequencing laboratories.

The Sunday Guardian spoke to several researchers and microbiologists, who claimed that the numbers of existing genome sequencing labs in India have sufficient infrastructure in order to understand the Covid-19 situation in India. “As long as we have an efficient surveillance system and an efficient sequencing system, we must consider that the genome sequencing labs have sufficient infrastructure. Currently, India is quite well-poised in its ability to do genome sequencing,” Dr Samiran Panda, the director of the National Aids Research Institute, ICMR, told this paper.

However, Dr Nishith Kumar Pal, Professor of Microbiology at Jagannath Gupta Institute of Medical Sciences & Hospital, Kolkata, also hinted at the fact that the samples and data are analysed by the software. During the second wave of Covid-19, a large number of cases had occurred. So, the number of genome sequencing labs appeared to be less. But, since Covid-19 cases are down, I believe that the labs in India are not inadequate.”

Asked about the challenges faced by the researchers, Dr Panda said, “The specimen needs to be collected and transported in such a manner that the genome remains intact and can be sequenced for further research. However, if someone is infected but is asymptomatic, they do not go to the hospital. In such circumstances, it is difficult to get clinical samples. Also, due to some unfortunate circumstances, if the genome gets destroyed, one cannot sequence it for further research. The collection, transportation of samples, facilities and trained human resources are still required. At each step, beginning from the collection to transportation of the samples, careful standard operating procedures (SOP) are required.”


Similarly, Dr Abhrajyoti Ghosh, an Associate Professor from Bose Institute, said, “There are several challenges faced by the researchers, such as sample transportation and storage, unavailability of reagents and their procurement, unavailability of skilled technical support and skilled Bioinformatic support.”

He also added, “Preservation of samples is crucial as RNA is more sensitive. As Covid-19 is an RNA virus, it remains a challenge to preserve samples at suitable conditions to keep viral RNA intact. Besides, RT-PCR analysis requires skilled technical hands, which is still lacking in large parts of India. The private diagnostic labs and government labs are working day and night to solve these issues, but more of such testing laboratories in the remote areas is extremely important.”

Prof Ghosh noted, “The time of testing is very important. One requires substantial viral load for easy detection of virus through different methods, including RT-PCR. Unfortunately, people are not either aware or not advised to undergo the test at the correct time. Doctors are always advising correctly, but awareness in people is still lacking largely in the rural area.”

Fortunately, healthcare care systems in India are advanced enough to provide data for scientists and researchers. The Indian SARS-CoV-2 Genomics Consortium (INSACOG) is a consortium of 28 National Laboratories to monitor the genomic variations in the SARS-CoV-2. It has jointly been initiated by the Union Health Ministry of Health, and the Department of Biotechnology (DBT) with the Council for Scientific & Industrial Research (CSIR) and the Indian Council of Medical Research (ICMR). It monitors the genomic variations in the SARS-CoV-2 by a sentinel sequencing effort and helps to comprehend the evolution and spread of the virus. Keeping in view the possibility of the third wave, it decided to increase the sequencing effort. As per the latest report, the total number of samples processed is 102880, the total number of samples sequenced is 1,02,880 and the total number of sequences analysed are 99,832.

Talking about the developments in the present situation, Dr Panda said, “The speed has ramped up. INSACOG and many labs, which are part of the network, are situated in various parts of India from where the samples are being collected and tested for genome sequencing. The speed of viral genome sequencing is also fine.”

However, Associate Professor, Ghosh suggested that the country needs more sequencing facilities to enhance the rapid detection/sequencing of a large number of samples. He further added, “Transportation of samples not only costs money, but also sometimes we lose (RNA get degraded/destroyed) samples during transportation.”

The numbers of samples being tested in one genomic laboratory depend on the capacity of a laboratory. Dr Panda said that it could vary from a few to 100 to further, depending on the kind of equipment being used by the lab. He said, “The cost of testing one sample ranges from Rs 6,000 to Rs 10,000 depending on the part of the gene which is sequenced, but the cost comes down when it is sequenced in bulk.”

Similarly, Dr Pal said that one laboratory has a capacity of testing 100-200 samples. However, some believe that the number of laboratories must be increased to reduce the workload. He suggested, “Good instruments are required from abroad, along with technically trained manpower. Young biologists must be trained in several parts of the country to fulfill the purpose.”


Currently, many states in India have started to set up genome sequencing laboratories as two cases of Omicron are reported from Karnataka. The state has completed the procedure of setting up four genome sequencing laboratories at Gulbarga Institute of Medical Sciences, Mysore Medical College, Belgaum Institute of Medical Sciences and the Bowring Institute of Medical Science. The centres will start receiving the samples soon.