First detection of SARS-CoV-2 Delta variant (B.1.617.2) in the wastewater of (Ahmedabad), India

Abstract

Contrary to the conventional genomic surveillance based on clinical samples (symptomatic patients), the wastewater-based genomic surveillance can identify all the variants shed by the infected individuals in the population, as it does also include RNA fragmented shredded by clinically escaped asymptomatic patients. We analyzed four samples to detect key mutations in the SARS-CoV-2 genome and track circulating variants in Ahmedabad during the first wave (Sep/ Nov 2020) and before the second wave (in Feb 2021) of COVID-19 in India. The analysis showed a total of 35 mutations in the spike protein across four samples categorized into 23 types. We noticed the presence of spike protein mutations linked to the VOC-21APR-02; B.1.617.2 lineage (Delta variant) with 57% frequency in wastewater samples of Feb 2021. The key spike protein mutations were T19R, L452R, T478K, D614G, & P681R and deletions at 22029 (6 bp), 28248 (6 bp), & 28271 (1 bp). Interestingly, these mutations were not observed in the samples of Sep and Nov 2020 but appeared before the devastating second wave of COVID-19, which started in early April 2021 in India, caused rapid transmission and deaths all over India. We found the genetic traces of the B.1.617.2 in samples of early Feb 2021 i.e., more than a month before the first clinically confirmed case of the same variant in March 2021 in Ahmedabad, Gujarat. The present study tells about the circulating variants in Ahmedabad and suggests early prediction VOCs employing the wastewater genomic surveillance approach that must be exploited at a large scale for effective COVID-19 management.HighlightsWhole-genome sequencing of SARS-CoV-2 from the WW samples was carried out.Variant of Concern (VoC: VOC-21APR-02; B.1.617.2) were detected in WW samples.WBE may detect prevalent SARS-CoV-2 variants and monitor their cryptic transmissionWW genomic surveillance can aid the decision-making system for public health policies.

Deep learning via LSTM models for COVID-19 infection forecasting in India

“…Maharashtra and Delhi are less certain since they had multiple peaks and outbreaks in the past. The second wave of infections in 2021 began in Maharashtra [88,89] which has been the state that held one of the most number of COVID-19 cases and novel daily infections (Tables 1-4) [15].…”

Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater

“…This bioanalytical approach was applied to IWW samples from different locations in Belgium to retrospectively monitor the emergence of each VOC at a population scale. To our knowledge, most pre-existing WBE applications on SARS-CoV-2 variants mainly focus on sequencing [ 29 , 34 , 35 , 36 , 37 ] and RT-qPCR [ 26 , 28 , 38 , 39 ]. Only a limited number of studies have applied dPCR to estimate the VOC circulation in IWW [ 25 , 27 , 40 , 41 ].…”

Differentiation of SARS-CoV-2 Variants Using RT-qPCRs by Targeting Recurrent Mutation Sites: A Diagnostic Laboratory Experience from Multi-Center Regional Study, August 2020–December 2021, Poland

“…The H655Y change enhances the transmissibility of the virus [ 20 ]. The Delta variant was first found in India in December 2020 [ 21 ], and it includes four substitutions of interest in the S protein, three new ones, L452R and T478K and P681R, and the D614G earlier observed in Alpha, Beta and Gamma [ 10 ]. These mutations reduce the ability to neutralize antibodies to recognize the virus and block infection [ 22 ].…”