Waste water sequencing analysis picked up key mutations of SARS-CoV-2: Study

The study provides evidence on how waste water sequencing identified mutations, and shows variants in circulation before being observed through clinical data.

A STUDY in Pune’s open wast water drains from December 2020 to March 2021 has not only been able to assess the presence of SARS-CoV-2 nucleic acid, but also picked up key mutations circulating in the community. The study provides evidence on how waste water sequencing identified mutations, and shows variants in circulation before being observed through clinical data.

Waste water sequencing analysis revealed mutations L452R and E484Q associated with B.1.617 lineage in samples collected during March. These mutations were absent in samples collected from December 2020 to February 2021.

“The study is significant as it is a first-of-its-kind in the country to test capability of waste water sequencing data to provide mutations in circulation before they are observed clinically. Through waste water epidemiology, we could identify mutations associated with SARS-CoV-2, and that can function as an early warning indicator system,” said Tanmay Dharmadhikari, Vinay Rajput and others from researchers from CSIR-NCL. The study was supported by funding from Science Engineering and Research Board (GoI), New Delhi, to researchers of CSIR-NCL.

In their paper ‘High throughput sequencing based detection of SARS-CoV-2 prevailing in waste water of Pune, West India’ posted as a preprint on medRxiV ( a non peer-reviewed platform) on June 9, scientists have said the tracking of genomic variants from waste water was essential to understand the spread. These findings will soon be communicated to a peer-reviewed journal.

The Indian Express on June 8 reported that a team of scientists from CSIR-National Chemical Laboratory had made an official presentation to Deputy Chief Minister Ajit Pawar on their pilot study that was able to detect the presence of SARS-CoV-2 RNA in sewage samples. Pune Municipal Commissioner Vikram Kumar had also indicated that they would continue the project for another year in anticipation of future waves of the Covid-19 pandemic. The funding for another year has been sanctioned as part of the CSIR project.

The study found all the waste water samples collected between December 2020 and March 2021 were positive for SARS-CoV-2 nucleic acid fragments. The analysis showed several mutations in multiple genomic regions of SARS-CoV-2 , said Dr Mahesh Dharne, scientist, biochemical sciences division, CSIR-NCL, and project coordinator of the pilot study. The Ecosan Services Foundation, an NGO, partnered in the study

In total, 108 mutations, categorised into 40 types based on nucleotide position, were detected in all samples. Notably, nine mutations in the spike region (L452R, C480R, E484Q, D614G, P681R, N801, D950N, Q1071H, P1140) were observed in this study.

The study also provided instances where there were four mutations (N801:C480R, NSP14:C279F and NSP3:L550del) obtained from waste water sequenced data, which are either not reported in GISAID (Global Initiative on Sharing All Influenza Data) from India or in case of novel mutation, not across the world.

A novel mutation NSP13:G206F mapping to the NSP13 region was also observed from waste water, the study said.

Regular monitoring of waste water is an essential criterion to observe mutations associated with concerned variants in circulation as the required results can be obtained from a smaller sample volume of wastewater than the more significant number of individuals , Dr Dharne said. The team also comprised Dr Syed Dastager and Dr Sanjay Kamble from NCL who ascertained that for polio and rotavirus tracking, waste water surveillance has been useful in the past.

Dr L S Shashidhara, one of the founders of Pune Knowledge Cluster, said it was an important study. “They have identified a variant at least two months before it was reported to be in patients’ samples. Environmental waste water surveillance is a strategy . It is able to predict ahead of time and tell us if a small surge is happening, which is not yet detected via traditional diagnostic methods so that we are better prepared,” he said.

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