02709nas a2200313   4500008004100000022001400041245011200055210006900167260000900236300001100245490000800256520169600264653001901960653001701979653001701996653002402013653001502037653001502052100002602067700001802093700002302111700002502134700001802159700001802177700002302195700002302218700002302241856013102264       2022                        eng d  a0048-969700aHigh throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India0 aHigh throughput sequencing based direct detection of SARSCoV2 fr  cFEB   a1510380 v8073 aGiven a large number of SARS-CoV-2 infected individuals, clinical detection has proved challenging. The wastewater-based epidemiological paradigm would cover the clinically escaped asymptomatic individuals owing to the faecal shedding of the virus. We hypothesised using wastewater as a valuable resource for analysing SARS-CoV-2 mutations circulating in the wastewater of Pune region (Maharashtra; India), one of the most affected during the covid-19 pandemic. We conducted study in open wastewater drains from December 2020- March 2021 to assess the presence of SARS-CoV-2 nucleic acid and further detect mutations using ARTIC protocol of MinION sequencing. The analysis revealed 108 mutations across six samples categorised into 39 types of mutations. We report the occurrence of mutations associated with Delta variant lineage in March-2021 samples, simultaneously also reported as a Variant of Concern (VoC) responsible for the rapid increase in infections. The study also revealed four mutations; S:N801, S:C480R, NSP14:C279F and NSP3:L550del not currently reported from wastewater or clinical data in India but reported worldwide. Further, a novel mutation NSP13:G206F mapping to NSP13 region was observed from wastewater. Notably, S:P1140del mutation was detected in December 2020 samples while it was reported in February 2021 from clinical data, indicating the instrumentality of wastewater data in early detection. This is the first study in India to demonstrate utility of sequencing in wastewater based epidemiology to identify mutations associated with SARS-CoV-2 virus fragments from wastewater as an early warning indicator system. (c) 2021 Elsevier B.V. All rights reserved.10aARTIC protocol10aEpidemiology10aMetagenomics10aNanopore sequencing10aSARS-CoV-210awastewater1 aDharmadhikari, Tanmay1 aRajput, Vinay1 aYadav, Rakeshkumar1 aBoargaonkar, Radhika1 aPatil, Dhawal1 aKale, Saurabh1 aKamble, Sanjay, P.1 aDastager, Syed, G.1 aDharne, Mahesh, S.  uhttps://library.ncl.res.in/content/high-throughput-sequencing-based-direct-detection-sars-cov-2-fragments-wastewater-pune-west