SARS-CoV-2 Variability in Patients and Wastewaters—Potential Immuno-Modulation during the Shift from Delta to Omicron DOI Creative Commons

Ahlam Chaqroun,

Cédric Hartard,

Thomas Josse

и другие.

Biomedicines, Год журнала: 2022, Номер 10(9), С. 2080 - 2080

Опубликована: Авг. 25, 2022

The continuous emergence of SARS-CoV-2 variants favors potential co-infections and/or viral mutation events, leading to possible new biological properties. aim this work was characterize genetic variability during the Delta-Omicron shift in patients and a neighboring wastewater treatment plant (WWTP) same urban area. surveillance performed by routine screening positive samples single nucleotide polymorphism analysis within S gene. Moreover, additionally national systematic whole genome sequencing (WGS) once week SARS-CoV-2-positive patients, WGS also applied when mutational profiles were difficult interpret screening. Thus, on 414 respiratory four samples, northeastern France. This allowed us report (i) temporally concordant Delta Omicron wastewaters; (ii) characterization 21J (Delta) 21K (Omicron)/BA.1-21L (Omicron)/BA.2-BA.4 mixtures from humans or environmental samples; (iii) mapping composite mutations predicted impact immune properties Spike protein.

Язык: Английский

Tracing COVID-19 Trails in Wastewater: A Systematic Review of SARS-CoV-2 Surveillance with Viral Variants DOI Open Access
Ananda Tiwari, Sangeet Adhikari, Shuxin Zhang

и другие.

Water, Год журнала: 2023, Номер 15(6), С. 1018 - 1018

Опубликована: Март 7, 2023

The emergence of new variants SARS-CoV-2 associated with varying infectivity, pathogenicity, diagnosis, and effectiveness against treatments challenged the overall management COVID-19 pandemic. Wastewater surveillance (WWS), i.e., monitoring infections in communities through detecting viruses wastewater, was applied to track spread globally. However, there is a lack comprehensive understanding use WWS for variants. Here we systematically reviewed published articles reporting different wastewater by following PRISMA guidelines provided current state art this study area. A total 80 studies were found that reported until November 2022. Most these (66 out 80, 82.5%) conducted Europe North America, resource-rich countries. There high variation sampling strategy around world, composite (50/66 studies, 76%) as primary method In contrast, grab more common (8/14 57%) resource-limited Among detection methods, reverse transcriptase polymerase chain reaction (RT-PCR)-based sequencing quantitative RT-PCR commonly used wastewater. variants, B1.1.7 (Alpha) variant appeared earlier pandemic most (48/80 studies), followed B.1.617.2 (Delta), B.1.351 (Beta), P.1 (Gamma), others All same pattern clinical within timeline, demonstrating tracked all timely way when emerged. Thus, may be utilized identify presence or absence follow development transmission existing emerging Routine powerful infectious disease tool implemented

Язык: Английский

Процитировано

40
Reviewing methods of deep learning for diagnosing COVID-19, its variants and synergistic medicine combinations DOI Open Access

Qandeel Rafique,

Ali Rehman,

Muhammad Sher Afghan

и другие.

Computers in Biology and Medicine, Год журнала: 2023, Номер 163, С. 107191 - 107191

Опубликована: Июнь 20, 2023

Язык: Английский

Процитировано

25
Early Detection of SARS-CoV-2 Omicron BA.4 and BA.5 in German Wastewater DOI Creative Commons
Alexander Wilhelm, Shelesh Agrawal,

Jens Schoth

и другие.

Viruses, Год журнала: 2022, Номер 14(9), С. 1876 - 1876

Опубликована: Авг. 25, 2022

Wastewater-based SARS-CoV-2 epidemiology (WBE) has been established as an important tool to support individual testing strategies. The Omicron sub-variants BA.4/BA.5 have spread globally, displacing the preceding variants. Due severe transmissibility and immune escape potential of BA.4/BA.5, early monitoring was required assess implement countermeasures in time. In this study, we monitored prevalence at six municipal wastewater treatment plants (WWTPs) Federal State North Rhine-Westphalia (NRW, Germany) May June 2022. Initially, L452R-specific primers/probes originally designed for Delta detection were validated using inactivated authentic viruses evaluated their suitability detecting BA.4/BA.5. Subsequently, assay used RT-qPCR analysis RNA purified from obtained twice a week WWTPs. occurrence L452R carrying detected 2022, presence confirmed by variant-specific single nucleotide polymorphism PCR (SNP-PCR) targeting E484A/F486V NGS sequencing. Finally, mutant fractions quantitatively digital PCR, confirming majority variant 5 conclusion, successive workflow RT-qPCR, SNP-PCR, RT-dPCR demonstrates strength WBE versatile rapidly monitor variants spreading independently test capacities.

Язык: Английский

Процитировано

19
Intensity of sample processing methods impacts wastewater SARS-CoV-2 whole genome amplicon sequencing outcomes DOI Creative Commons
Shuchen Feng, Sarah M. Owens, Abhilasha Shrestha

и другие.

The Science of The Total Environment, Год журнала: 2023, Номер 876, С. 162572 - 162572

Опубликована: Март 3, 2023

Язык: Английский

Процитировано

11
Hyperplex PCR enables highly multiplexed analysis of point mutations in wastewater: long-term SARS-CoV-2 variant surveillance in Sweden as a case study DOI
Ruben R. G. Soares,

Javier Edo Varg,

Attila Szabó

и другие.

Water Research, Год журнала: 2025, Номер 274, С. 123154 - 123154

Опубликована: Янв. 16, 2025

Язык: Английский

Процитировано

0
Diagnostic performance of allele-specific RT-qPCR and genomic sequencing in wastewater-based surveillance of SARS-CoV-2 DOI Creative Commons

Md Pervez Kabir,

Élisabeth Mercier,

Walaa Eid

и другие.

Eco-Environment & Health, Год журнала: 2025, Номер 4(1), С. 100135 - 100135

Опубликована: Янв. 21, 2025

Clinical genomic surveillance is regarded as the gold standard for monitoring SARS-CoV-2 variants globally. However, pandemic wanes, reduced testing poses a risk to effectively tracking trajectory of these within populations. Wastewater-based that estimates variant frequency based on its defining set alleles derived from clinical has been successfully implemented. This method challenges, and allele-specific (AS) RT-qPCR or RT-dPCR may instead be used complementary estimating prevalence. Demonstrating equivalent performance methods prerequisite their continued application in current future pandemics. Here, we compared single-allele using AS-RT-qPCR, haplotype estimations amplicon-based sequencing estimate prevalence wastewater during emergent prevalent periods Delta, Omicron, two sub-lineages Omicron. We found all three estimation were concordant contained sufficient information describe further confirmed accuracy by quantifying diagnostic through Youden's index. The index AS-RT-qPCR was low period particular while same allele negatively influenced due insufficient read depth. haplotype-based calls when common between variants. Coupling with can overcome shortcomings either platform provide comprehensive picture stakeholders public health responses.

Язык: Английский

Процитировано

0
An improved method for determining frequency of multiple variants of SARS-CoV-2 in wastewater using qPCR assays DOI Open Access
Meghan Fuzzen, Nathanael B.J. Harper, Hadi A. Dhiyebi

и другие.

The Science of The Total Environment, Год журнала: 2023, Номер 881, С. 163292 - 163292

Опубликована: Апрель 7, 2023

Язык: Английский

Процитировано

10
In Silico Protein Folding Prediction of COVID-19 Mutations and Variants DOI Creative Commons
Sumana Bhowmick, Tim Jing, Wei Wang

и другие.

Biomolecules, Год журнала: 2022, Номер 12(11), С. 1665 - 1665

Опубликована: Ноя. 10, 2022

With its fast-paced mutagenesis, the SARS-CoV-2 Omicron variant has threatened many societies worldwide. Strategies for predicting mutagenesis such as computational prediction of structural diversity and interaction with human receptor will greatly benefit our understanding virus help develop therapeutics against it. We aim to use protein structure algorithms along molecular docking study effects various mutations in Receptor Binding Domain (RBD) key interactions angiotensin-converting enzyme 2 (ACE-2) receptor. The RBD structures naturally occurring variants were generated from WUHAN-Hu-1 using trRosetta algorithm. Docking (HADDOCK) binding analysis (PRODIGY) between predicted sequences ACE-2 highlighted at Receptor-Binding Motif (RBM). Further conserved residues Original, Delta, (P499S T500R) demonstrated stronger T500R mutation underwent some preliminary tests vitro transmissibility cells; results correlate in-silico analysis. In summary, we suggest P499 T500 potential sites that could increase affinity yet do not exist nature. This work demonstrates algorithm predict future RBM SARS-CoV-2, followed by experimental testing further efficacy verification. It is important understand folding therapeutics.

Язык: Английский

Процитировано

14
Wastewater-based epidemiology: Retrospective, current status, and future prospects DOI
Vincent Maréchal, Yvon Maday, Clémentine Wallet

и другие.

Anaesthesia Critical Care & Pain Medicine, Год журнала: 2023, Номер 42(5), С. 101251 - 101251

Опубликована: Май 24, 2023

Язык: Английский

Процитировано

8
Delineating the Spread and Prevalence of SARS-CoV-2 Omicron Sublineages (BA.1–BA.5) and Deltacron Using Wastewater in the Western Cape, South Africa DOI
Rabia Johnson,

Noluxabiso Mangwana,

Jyoti Sharma

и другие.

The Journal of Infectious Diseases, Год журнала: 2022, Номер 226(8), С. 1418 - 1427

Опубликована: Авг. 26, 2022

Abstract This study was one of the first to detect Omicron sublineages BA.4 and BA.5 in wastewater from South Africa. Spearman rank correlation analysis confirmed a strong positive between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral RNA samples clinical cases (r = 0.7749, P < .0001). SARS-CoV-2 load detected wastewater, resulting Delta-driven third wave, significantly higher than during Omicron-driven fourth wave. Whole-genome sequencing presence lineage defining mutations with occurrence reported 23 November 2021 (BA.1 predominant). The variant spread rapidly, prevalence Omicron-positive rising >80% by 10 January 2022 BA.2 as predominant sublineage March 2022, whilst on 18 April were selected sites. These findings demonstrate value wastewater-based epidemiology monitor spatiotemporal potential origin new sublineages.

Язык: Английский

Процитировано

12