Wastewater and marine bioindicators surveillance to anticipate COVID-19 prevalence and to explore SARS-CoV-2 diversity by next generation sequencing: One-year study

Novoa, Beatriz; Ríos-Castro, Raquel; Otero-Muras, Irene; Gouveia, Susana; Cabo, Adrián; Saco, Amaro; Rey-Campos, Magalí; Pájaro, Manuel; Fajar, Noelia M.; Aranguren, Raquel; Romero, Alejandro; Panebianco, Antonella; Valdés, Lorena; Payo, Pedro; Alonso, Antonio A.; Figueras, António; Cameselle, Claudio

doi:10.1016/j.scitotenv.2022.155140

Cited by 17 publications

(17 citation statements)

References 47 publications

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“…The copyright holder for this preprint this version posted March 6, 2023. ; https://doi.org/10.1101/2023.03.02.23286683 doi: medRxiv preprint matter would be vastly diluted by the addition of household sewage water and rain, establishing a probability framework for detecting viral fragments (Novoa et al, 2022;Wade et al, 2022). We detected SARS-CoV-2 in 100% of qRT-PCR negative samples, concluding that the amplicon sequencing protocol is much more sensitive in detecting the SARS-CoV-2 fragments in sewage water than qRT-PCR.…”

Section: Discussionmentioning

confidence: 99%

“…Initially, researchers depended on qRT-PCR and Sanger sequencing to establish the existence of viral fragments of SARS-CoV-2 in wastewater. WBE studies are founded on SARS-CoV-2 fecal shedding (Crank et al, 2022; Li et al, 2022); however, the fecal matter would be vastly diluted by the addition of household sewage water and rain, establishing a probability framework for detecting viral fragments (Novoa et al, 2022; Wade et al, 2022). We detected SARS-CoV-2 in 100% of qRT-PCR negative samples, concluding that the amplicon sequencing protocol is much more sensitive in detecting the SARS-CoV-2 fragments in sewage water than qRT-PCR.…”

Section: Discussionmentioning

confidence: 99%

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Campus Sewage Water Surveillance based dynamics and infection trends of SARS-CoV-2 variants during third wave of COVID-19 in Pune, India

Malik

Rajput

Pramanik

et al. 2023

Preprint

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The wastewater-based epidemiology (WBE) of SARS-CoV-2 is a quick and cost-effective method of tracking virus transmission. However, few studies reported on campus or in academic or residential settings worldwide. In this study, we demonstrated the WBE approach to detect, monitor, and evaluate genomic variants of SARS-CoV-2 fragments in a sewage treatment plant (STP) located on the campus of CSIR National Chemical Laboratory, Pune, India. Herein we describe the early warning capability of WBE, with viral load rise in campus sewage water up to 14 days before its clinical detection. This was supported further by a significant correlation between SARS-CoV-2 RNA concentration and clinically reported COVID-19 cases on campus. Additionally, we comprehended the probable targets missed by the quantitative qRT-PCR using amplicon-based sequencing due to low viral load. The analysis revealed the presence of signature mutations of the Omicron (S:N679K, S:N764K, S:D796Y, N:P13L, ORF1a:T3255I, ORF1a:K856R, ORF1a:P3395H, and N:S413R) before the lineage was first detected globally. Further, we used Lineage decomposition (LCS) tool to detect the Variant of Concern (VOC)/Variant of Interest (VOI) signals upto a month earlier in sewage water samples. The analysis also indicated the transition of lineage from Delta to Omicron in late Decemeber,2021. This is the first study in India highlighting the use of on-campus STP to evaluate the local spread of SARS-CoV-2, which could aid in preventing COVID-19 in academic institutes/universities. This study proves the usefulness of WBE as an early warning system for detecting, tracking and tracing VOCs using the sequencing approach. The current study could aid in taking critical decisions to tackle the pandemic scenario on campus.HighlightsThe first study on campus sewage water for SARS-CoV-2 surveillance in IndiaEarly detection of Omicron VOC signals during early November 2021Sequencing revealed the presence of Omicron VOC fragments prior to clinical cases reported on campusGenomic analysis indicated transition of Delta to Omicron lineage in late December 2021 and potentially led to the third waveCombining qRT-PCR and sequencing could be useful for on-campus tracking of variants using wastewater surveillance

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Campus Sewage Water Surveillance based dynamics and infection trends of SARS-CoV-2 variants during third wave of COVID-19 in Pune, India

Malik

Rajput

Pramanik

et al. 2023

Preprint

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“…According with SIR models for infectious diseases [3], we assume that the N individuals of the total population can be split into the three categories S I and R previously described. These three categories can be associated to the corresponding three model state variables, which are related through the following set of reactions [4,5]:…”

Section: Mathematical Modelingmentioning

confidence: 99%

“…In this context, we reinterpret the transitions between each possible state of a SIR model (Susceptible, Infected, Recovered) as chemical reactions. This system is modelled using a Chemical Master Equation (CME) which incorporates the inherent stochasticity of the COVID-19 infection process [4,5]. We have tested this technique for small and medium municipalities in Galicia using data of the Public Health System (SERGAS) and data of viral load in Wastewater Treatment Plants (WWTP).…”

Section: Introductionmentioning

confidence: 99%

“…The population is split in Susceptible, Total Infected (estimated from the viral load in WWTP), Observed (detected by SERGAS) and Recovered. We construct the associated CME and solve it via the SSA, which allows forecasting the evolution of the number of infected persons starting from the viral load detected in sewage the previous week [4,5].…”

Section: Introductionmentioning

confidence: 99%

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Chemical Master Equation model to predict the COVID-19 epidemic spread

Pájaro¹,

Alonso²,

Otero-Muras³

Kalpa Publications in Computing

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The COVID-19 pandemics has shown relevant stochasticity in the spread of viral in- fection. Here, we formulate the dynamics of the epidemics spread as a stochastic SIR model, handling the compartmental model (of the SIR type) as a set of chemical reactions, and applying the Chemical Master Equation that describes the dynamics of the equivalent stochastic chemical reaction system. In this way, the solution (evolution of the probability distribution over time) can be obtained via the classical Stochastic Simulation Algorithm. The proposed methodology has been used to predict the COVID-19 evolution in small and medium size municipalities of Galicia.

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Wastewater treatment risks and challenges for public health and the environment during the Covid‐19 pandemic: a review

Kokkinos

Venieri

Mantzavinos

2023

J of Chemical Tech & Biotech

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During the coronavirus disease 2019 (COVID‐19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), viral transport, fate, disinfection and environmental release in wastewater treatment plants have been issues of high importance for overall management. Although a huge number of scientific publications related to coronaviruses have been published, the number of studies on different aspects of wastewater treatment strategies to deal with SARS‐CoV‐2 abatement is still relatively limited and results are often confusing. To define real wastewater risks for public health and the environment, we have performed a systematic review and identified 96 papers from the PubMed database. We focused on SARS‐CoV‐2 wastewater treatments and how the type and level of treatments affect the virological quality of the effluents, the role of disinfectants, the treatment of medical wastewater, the role of new technologies, as well as the wastewater treatment in low‐ and middle‐income countries. It was concluded that, in general, well‐designed and well‐functioning wastewater treatment plants (WWTPs) and on‐site reliable sanitation systems may significantly limit the risk of SARS‐CoV‐2. The development of cost‐effective decentralized water and wastewater treatment facilities for low‐ and middle‐income countries for the abatement of coronaviruses should be enhanced. Lessons learned during the COVID‐19 pandemic with regard to wastewater treatment are expected to support an improved detection, response and containment of future viral disease outbreaks. © 2023 The Authors. Journal of Chemical Technology and Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry (SCI).

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Wastewater and marine bioindicators surveillance to anticipate COVID-19 prevalence and to explore SARS-CoV-2 diversity by next generation sequencing: One-year study

Cited by 17 publications

References 47 publications

Campus Sewage Water Surveillance based dynamics and infection trends of SARS-CoV-2 variants during third wave of COVID-19 in Pune, India

Campus Sewage Water Surveillance based dynamics and infection trends of SARS-CoV-2 variants during third wave of COVID-19 in Pune, India

Chemical Master Equation model to predict the COVID-19 epidemic spread

Wastewater treatment risks and challenges for public health and the environment during the Covid‐19 pandemic: a review

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