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

Joshi, Madhvi; Kumar, Manish; Srivastava, Vaibhav; Kumar, Dinesh; Rathore, Dalip Singh; Pandit, Ramesh; Graham, David W.; Joshi, Chaitanya

doi:10.1016/j.envpol.2022.119757

Cited by 26 publications

(16 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Then, a positive clinical sample for SARS-CoV-2, with 7.3 × 10 6 gene copies/L (GC/L) was employed. The recovery efficiency of SARS-CoV-2 was assessed in this study using bovine coronavirus (BCoV) based on its gene copies quantified by RT-qPCR (Joshi et al, 2022) (Table 2). To verify primer-primer dimer and false-positive results, a melt curve was used before the analysis.…”

Section: Results Validation and Quality Controlmentioning

confidence: 99%

A 30-day follow-up study on the prevalence of SARS-COV-2 genetic markers in wastewater from the residence of COVID-19 patient and comparison with clinical positivity

Islam

Rahman²,

Jakariya³

et al. 2023

Science of The Total Environment

View full text Add to dashboard Cite

Section: Results Validation and Quality Controlmentioning

confidence: 99%

A 30-day follow-up study on the prevalence of SARS-COV-2 genetic markers in wastewater from the residence of COVID-19 patient and comparison with clinical positivity

Islam

Rahman²,

Jakariya³

et al. 2023

Science of The Total Environment

View full text Add to dashboard Cite

“…We collected 442 wastewater samples from 10 locations, representing an estimated 7.4 million individuals. WBE has been used in several studies globally to identify and quantify the SARS-CoV-2 fragments in wastewater (Srivastava et al, 2021; Dharmadhikari et al, 2022; Joshi et al, 2022; Jahn et al, 2022; Morvan et al, 2022). By applying this model at the city level, we aim to prevent the spread of COVID-19 and better understand the dynamics of SARS-CoV-2 transmission in Pune city.…”

Section: Discussionmentioning

confidence: 99%

“…These studies provides essential information on the detection, quantification and genetic characterization of SARS-CoV-2 in sewage samples (Srivastava et al, 2021; Dharmadhikari et al, 2022; Lamba et al, 2023). The WBE has the potential to detect viral signals earlier than clinical surveillance methods and can offer a less biased assessment of viral heterogeneity and public health (Joshi et al, 2022; Jahn et al, 2022; Morvan et al, 2022). The ongoing COVID-19 outbreak has brought attention to the need for rapid and accurate surveillance of the spread of SARS-CoV-2.…”

Section: Introductionmentioning

confidence: 99%

Genomic surveillance reveals early detection and transition of Delta to Omicron Lineages of SARS-CoV-2 Variants in wastewater treatment plants of Pune, India

Rajput

Pramanik

Malik

et al. 2023

Preprint

View full text Add to dashboard Cite

The COVID-19 pandemic has emphasized the urgency for rapid public health surveillance methods in early detection and monitoring of the transmission of infectious diseases. The wastewater-based epidemiology (WBE) has emerged as a promising tool to analyze and enumerate the prevalence of infectious pathogens in a population ahead of time. In the present study, real time quantitative polymerase chain reaction (RT-qPCR) and Illumina sequencing was performed to determine the SARS-CoV-2 load trend and dynamics of variants over a longitudinal scale in 442 wastewater (WW) samples collected from 10 sewage treatment plants (STPs) of Pune city, India, during November 2021 to April-2022. In total 426 distinct lineages representing 17 highly transmissible variants of SARS-CoV-2 were identified. The SARS-CoV-2 Omicron variant fragments were detected in WW samples prior to its detection in clinical cases. Moreover, highly contagious sub-lineages of Omicron, such as BA.2.12 (0.8-0.25%), BA.2.38 (0.8-1.0%), BA.2.75 (0.01-0.02%), BA.3 (0.09-6.3%), BA.4 (0.24-0.29%), and XBB (0.01-13.7%) fragments were significantly detected. The longitudinal analysis also suggested the presence of the BA.5 lineage in November 2021, which was not reported in the clinical settings throughout the duration of this study, indicative of silent variant persistence. Overall, the present study demonstrated the practicality of WBE in early detection of SARS CoV-2 variants, which could be useful in tracking future outbreaks of SARS-CoV-2. Such approaches could be implicated in the monitoring of the infectious agents before they appear in clinical cases.

show abstract

“…In contrast to humans, where only respiratory and oral droplets serve as the main source of infection, both respiratory and fecal secretions of animals may act as important sources of the infection and an additional source of the virus for environmental contamination and transmission [ 11 ]. Previously, our group also showed proof of surveillance of SARS-CoV-2 through wastewater systems [ 27 ] and, for the first time, reported the presence of SARS-CoV-2 delta variant B.1.617.2 in the wastewater system [ 15 ].…”

Section: Discussionmentioning

confidence: 99%

“…The representative samples that yielded low Ct values and, consequently, high viral RNA loads were further subjected to whole-genome sequencing using the IonGeneStudio S5 plus system and SARS-CoV-2 Research Panel (Thermo Fisher Scientific, Pleasanton, CA, USA). For this, the method we follow is the same as described in our previous study [ 15 ]. The data was analyzed using CLC genomics workbench v 12.0.3.…”

Section: Methodsmentioning

confidence: 99%

Surveillance and Molecular Characterization of SARS-CoV-2 Infection in Non-Human Hosts in Gujarat, India

Kumar

Antiya

Patel

et al. 2022

IJERPH

Self Cite

View full text Add to dashboard Cite

Since December 2019, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has been spreading worldwide, triggering one of the most challenging pandemics in the human population. In light of the reporting of this virus in domestic and wild animals from several parts of the world, a systematic surveillance study was conceptualized to detect SARS-CoV-2 among species of veterinary importance. Nasal and/or rectal samples of 413 animals (dogs n= 195, cattle n = 64, horses n = 42, goats n = 41, buffaloes n = 39, sheep n = 19, cats n = 6, camels n = 6, and a monkey n = 1) were collected from different places in the Gujarat state of India. RNA was extracted from the samples and subjected to RT-qPCR-based quantification of the target sequences in viral nucleoprotein (N), spike (S), and ORF1ab genes. A total of 95 (23.79%) animals were found positive, comprised of n = 67 (34.35%) dogs, n= 15 (23.43%) cattle, and n = 13 (33.33%) buffaloes. Whole SARS-CoV-2 genome sequencing was done from one sample (ID-A4N, from a dog), where 32 mutations, including 29 single-nucleotide variations (SNV) and 2 deletions, were detected. Among them, nine mutations were located in the receptor binding domain of the spike (S) protein. The consequent changes in the amino acid sequence revealed T19R, G142D, E156-, F157-, A222V, L452R, T478K, D614G, and P681R mutations in the S protein and D63G, R203M, and D377Y in the N protein. The lineage assigned to this SARS-CoV-2 sequence is B.1.617.2. Thus, the present study highlights the transmission of SARS-CoV-2 infection from human to animals and suggests being watchful for zoonosis.

show abstract

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

Cited by 26 publications

References 38 publications

A 30-day follow-up study on the prevalence of SARS-COV-2 genetic markers in wastewater from the residence of COVID-19 patient and comparison with clinical positivity

A 30-day follow-up study on the prevalence of SARS-COV-2 genetic markers in wastewater from the residence of COVID-19 patient and comparison with clinical positivity

Genomic surveillance reveals early detection and transition of Delta to Omicron Lineages of SARS-CoV-2 Variants in wastewater treatment plants of Pune, India

Surveillance and Molecular Characterization of SARS-CoV-2 Infection in Non-Human Hosts in Gujarat, India

Contact Info

Product

Resources

About