High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India

Dharmadhikari, Tanmay; Rajput, Vinay; Yadav, Rakeshkumar; Boargaonkar, Radhika; Patil, Dhawal; Kale, Saurabh; Kamble, Sanjay P.; Dastager, Syed G.; Dharne, Mahesh

doi:10.1016/j.scitotenv.2021.151038

Cited by 35 publications

(39 citation statements)

References 25 publications

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“…Our results are similar to Dharmadhikari et al (2022) , who performed MinION sequencing of SARS-CoV-2 fragments in wastewater of Pune, West India, from December 2020–March 2021. The results suggested 108 mutations in six samples grouped into 39 categories and were associated with Delta variant lineage in March-2021 clinical samples.…”

Section: Resultssupporting

confidence: 88%

“…D1118H, D614G, H69del, N501Y, P681H, S982A, and T716I) were present in all the samples A570D and Y144del were identified in 53 samples. Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2), and Gamma (P.1) Agrawal et al (2022) Pune, India Dec 2020 to Mar 2021 Wastewater cDNA synthesis/nanopore library preparation (MinION sequencing) P1140del, L452R E484Q, D614G; Q1071H, C480R, D950N, N801, P681R Delta (B.1.617.1) Dharmadhikari et al (2022) Spain Apr 2020 to Jan 2021 Sewage (76 samples) cDNA synthesis/Illumina MiSeq platform by paired-end reads (2 × 200) A total of 627 nucleotide substitutions and 20 deletions. During first and second wave: 8 deletions detected, with 5 of them in the (Δ21–23, Δ82–84, Δ84–86, Δ141–143, and Δ682); one in the spike glycoprotein (Δ385); and two in the ORF3a (Δ80 and Δ11–20).…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Genetic sequencing detected the SARS-CoV-2 delta variant in wastewater a month prior to the first COVID-19 case in Ahmedabad (India)

Joshi

Kumar

Srivastava

et al. 2022

Environmental Pollution

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Section: Resultssupporting

confidence: 88%

Section: Resultsmentioning

confidence: 99%

Genetic sequencing detected the SARS-CoV-2 delta variant in wastewater a month prior to the first COVID-19 case in Ahmedabad (India)

Joshi

Kumar

Srivastava

et al. 2022

Environmental Pollution

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“…Massive parallel sequencing techniques applied to sewage samples allow us to analyze a large number of SARS-CoV-2 genomes, including those present in symptomatic and asymptomatic persons. Through the analysis of sequences, it is possible to detect low-frequency variants (LFV) and to infer which lineages are circulating at a certain time and place ( Bar-Or et al, 2021 ; Crits-Christoph et al, 2021 ; Dharmadhikari et al, 2021 ; Herold et al, 2021 ; Izquierdo-Lara et al, 2021 ; La Rosa et al, 2021 ; Nemudryi et al, 2020 ; Rios et al, 2021 ). Additionally, genomic analyses may allow to detect the entry of described lineages or Variants of Concern (VOCs) into populations, as well as the appearance of emerging lineages, to characterize new outbreaks, and to aid in viral strains tracking ( Bar-Or et al, 2021 ; Crits-Christoph et al, 2021 ; Izquierdo-Lara et al, 2021 ; La Rosa et al, 2021 ; Nemudryi et al, 2020 ; Rios et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Spatial and temporal distribution of SARS-CoV-2 diversity circulating in wastewater

et al. 2022

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Wastewater-based epidemiology (WBE) has proven to be an effective tool for epidemiological surveillance of SARS-CoV-2 during the current COVID-19 pandemic. Furthermore, combining WBE together with high-throughput sequencing techniques can be useful for the analysis of SARS-CoV-2 viral diversity present in a given sample. The present study focuses on the genomic analysis of SARS-CoV-2 in 76 sewage samples collected during the three epidemiological waves that occurred in Spain from 14 wastewater treatment plants distributed throughout the country. The results obtained demonstrate that the metagenomic analysis of SARS-CoV-2 in wastewater allows the detection of mutations that define the B.1.1.7 lineage and the ability of the technique to anticipate the detection of certain mutations before they are detected in clinical samples. The study proves the usefulness of sewage sequencing to track Variants of Concern that can complement clinical testing to help in decision-making and in the analysis of the evolution of the pandemic.

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“…The majority of the studies included in the review used 24 h composite sampling of influent. Grab samples were adopted by eleven groups, with volumes ranging from 200 to 1000 mL [ 20 , 25 , 30 , 33 , 34 , 40 , 41 , 44 , 46 , 48 , 52 ]. Grab sampling is fast but unreliable, as it captures only a defined time point, and the use should be considered based on sampling facility and expected outcome, e.g., during morning hygiene in hospital [ 49 ].…”

Section: Methodsmentioning

confidence: 99%

“…Immediately after transportation to the laboratory, infectious agents in wastewater are inactivated at 60 °C for 90 min [ 29 , 46 ]. In experiments using surrogate viruses, no loss of RNA yield was noticed with treatment for 30 min at 56 °C [ 51 ].…”

Section: Methodsmentioning

confidence: 99%

Wastewater Sequencing—An Innovative Method for Variant Monitoring of SARS-CoV-2 in Populations

Tamáš

Potocarova

Konečná

et al. 2022

IJERPH

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The SARS-CoV-2 outbreak has already affected more than 555 million people, and 6.3 million people have died. Due to its high infectivity, it is crucial to track SARS-CoV-2 outbreaks early to prevent the spread of infection. Wastewater monitoring appears to be a powerful and effective tool for managing epidemiological situations. Due to emerging mutations of SARS-CoV-2, there is a need to monitor mutations in order to control the pandemic. Since the sequencing of randomly chosen individuals is time-consuming and expensive, sequencing of wastewater plays an important role in revealing the dynamics of infection in a population. The sampling method used is a crucial factor and significantly impacts the results. Wastewater can be collected as a grab sample or as a 24 h composite sample. Another essential factor is the sample volume, as is the method of transport used. This review discusses different pretreatment procedures and RNA extraction, which may be performed using various methods, such as column-based extraction, TRIzol, or magnetic extraction. Each of the methods has its advantages and disadvantages, which are described accordingly. RT-qPCR is a procedure that confirms the presence of SARS-CoV-2 genes before sequencing. This review provides an overview of currently used methods for preparing wastewater samples, from sampling to sequencing.

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High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India

Cited by 35 publications

References 25 publications

Genetic sequencing detected the SARS-CoV-2 delta variant in wastewater a month prior to the first COVID-19 case in Ahmedabad (India)

Genetic sequencing detected the SARS-CoV-2 delta variant in wastewater a month prior to the first COVID-19 case in Ahmedabad (India)

Spatial and temporal distribution of SARS-CoV-2 diversity circulating in wastewater

Wastewater Sequencing—An Innovative Method for Variant Monitoring of SARS-CoV-2 in Populations

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