Double mutant SARS-CoV-2 virus found in over 60 percent of samples in Maharashtra survey

Double mutation has been detected in 61 percent of the total 361 COVID-19 samples tested between January and March this year, a genome sequencing expert claimed on Wednesday even as he raised doubts over the methods of sample collection being adopted by authorities in Maharashtra, which is worst affected by the pandemic. However, experts in the fields of genome sequencing and cell science have observed that such a small sample size cannot be considered as an indication of the spread of the mutated virus. These 361 samples were tested at the genome sequencing laboratories in Maharashtra. On the other hand, authorities and officials of civic bodies that are collecting COVID-19 samples daily have complained about the lack of communication from the genome sequencing laboratories in Maharashtra as well as from the Centre about their findings on the sample analysis. This lack of communication is resulting in civic bodies and state health officials remaining in the dark and thus unable to come up with a better strategy to curb the rapid spread of coronavirus in Maharashtra, they said. “I am told that out of 361 COVID-19 samples tested by the National Institute of Virology in Pune, 61 per cent had the double mutation. However, this sample size is too small to conclude as Maharashtra has been conducting nearly two lakh tests per day. One should not take such a small sample size as an indication that the mutated virus is widespread,” a senior genome sequencing expert told PTI. Maharashtra is witnessing an unprecedented spike in coronavirus positive cases for the last few weeks. As of Tuesday, the cumulative tally of the infections in Maharashtra, the worst-hit state in India, stood at 35,19,208 while the death toll stood at 58,526, as per the state health department. Maharashtra had 5,93,042 active cases as of Tuesday. “Concerns were raised recently about the methods of sample collection being adopted by civic bodies and local health officials who are conducting daily COVID-19 tests,” the expert said. Stressing that the sample collection has to be random, he said the double mutation was found in all samples from a particular set of samples sent from Nashik. “Some 10 samples were sent from Nashik. When we inquired about the method used in collecting these samples, we found that local officials had sent 10 consecutive samples for genome sequencing. The sample selection has to be random to assess where exactly the mutated virus is found,” he said. In the case of Nashik, it means that these samples could be of the members of a big joint family. “Another possibility is that the people could be from the same area. (sample collection which is done in such a manner) completely defeats the purpose of random sampling and the genome sequencing efforts,” he added. The expert PTI spoke to works with a genome sequencing laboratory. Genome sequencing is the process of determining the entirety, or nearly the entirety, of the DNA sequence of an organism’s genome at a single time. Brihanmumbai Municipal Corporation (BMC) Additional Commissioner Suresh Kakani said that samples are being sent regularly to genome sequencing laboratories, “but we are not receiving any communication from them”. “We still do not know whether the sent samples contain the double mutation of the novel coronavirus or whether it is the earlier variant. If genome sequencing identifies the presence of double mutant virus (technically known as B.1.617) in the samples, in that event, we can issue revised guidelines to minimise its spread as it is more infectious,” Kakani said. He said the need of the hour is a regular update from the Centre or the consortium of ten laboratories set up for genome sequencing (by the Union government). Known as the “Indian SARS-CoV-2 Consortium on Genomics (INSACOG), it has identified two important mutations in the coronavirus variant dubbed as a “double mutant”. So far, the double mutant has been reported in various countries. Meanwhile, another senior scientist in the field of genomic sequencing claimed the consortium is still not fully operational “as there is a huge communication gap among the member laboratories”. “Unless the communication is smooth, it will take a longer time for the state machinery to know whether they are dealing with an old variant of COVID-19 or an infectious one. We are lucky that the virus is not mutated yet and not become lethal. “We cannot afford to learn about the status of the virus so late due to the lack of communication between these laboratories that have a common goal of genome sequencing,” he said.