scholarly journals Monitoring SARS-CoV-2 variants alterations in Nice neighborhoods by wastewater nanopore sequencing

2021 ◽  
Author(s):  
Geraldine Rios ◽  
Caroline Lacoux ◽  
Vianney Leclercq ◽  
Anna Diamant ◽  
Kevin Lebrigand ◽  
...  
Keyword(s):  
Treatment Plant ◽  
Low Frequency ◽  
Disease Outbreaks ◽  
Clinical Samples ◽  
Nanopore Sequencing ◽  
Infectious Disease Outbreaks ◽  
Epidemiological Tool ◽  
Frequency Comparison ◽  
Wastewater Samples ◽  
The City

Background: Wastewater surveillance has been proposed as an epidemiological tool to define the prevalence and evolution of the SARS-CoV-2 epidemics. However, most implemented SARS-CoV-2 wastewater surveillance projects were relying on qPCR measurement of virus titers and did not address the mutational spectrum of SARS-CoV-2 circulating in the population. Methods: We have implemented a nanopore RNA sequencing monitoring system in the city of Nice (France, 550,000 inhabitants). Between October 2020 and March 2021, we monthly analyzed the SARS-CoV-2 variants in 113 wastewater samples collected in the main wastewater treatment plant and 20 neighborhoods. Findings: We initially detected the lineages predominant in Europe at the end of 2020 (B.1.160, B.1.177, B.1.367, B.1.474, and B.1.221). In January, a localized emergence of a variant (Spike:A522S) of the B.1.1.7 lineage occurred in one neighborhood. It rapidly spread and became dominant all over the city. Other variants of concern (B.1.351, P.1) were also detected in some neighborhoods, but at low frequency. Comparison with individual clinical samples collected during the same week showed that wastewater sequencing correctly identified the same lineages as those found in COVID-19 patients. Interpretation: Wastewater sequencing allowed to document the diversity of SARS-CoV-2 sequences within the different neighborhoods of the city of Nice. Our results illustrate how sequencing of sewage samples can be used to track pathogen sequence diversity in the current pandemics and in future infectious disease outbreaks.

scholarly journals A Highly Automated Mobile Laboratory for On-site Molecular Diagnostics in the COVID-19 Pandemic

2021 ◽  
Vol 67 (4) ◽  
pp. 672-683
Author(s):  
Wanli Xing ◽  
Jiadao Wang ◽  
Chao Zhao ◽  
Han Wang ◽  
Liang Bai ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Nucleic Acid ◽  
Limit Of Detection ◽  
Disease Outbreaks ◽  
Clinical Samples ◽  
Acid Extraction ◽  
Robot Arm ◽  
Mobile Laboratory ◽  
Infectious Disease Outbreaks ◽  
Specimen Collection

Abstract Background Infectious disease outbreaks such as the COVID-19 (coronavirus disease 2019) pandemic call for rapid response and complete screening of the suspected community population to identify potential carriers of pathogens. Central laboratories rely on time-consuming sample collection methods that are rarely available in resource-limited settings. Methods We present a highly automated and fully integrated mobile laboratory for fast deployment in response to infectious disease outbreaks. The mobile laboratory was equipped with a 6-axis robot arm for automated oropharyngeal swab specimen collection; virus in the collected specimen was inactivated rapidly using an infrared heating module. Nucleic acid extraction and nested isothermal amplification were performed by a “sample in, answer out” laboratory-on-a-chip system, and the result was automatically reported by the onboard information platform. Each module was evaluated using pseudovirus or clinical samples. Results The mobile laboratory was stand-alone and self-sustaining and capable of on-site specimen collection, inactivation, analysis, and reporting. The automated sampling robot arm achieved sampling efficiency comparable to manual collection. The collected samples were inactivated in as short as 12 min with efficiency comparable to a water bath without damage to nucleic acid integrity. The limit of detection of the integrated microfluidic nucleic acid analyzer reached 150 copies/mL within 45 min. Clinical evaluation of the onboard microfluidic nucleic acid analyzer demonstrated good consistency with reverse transcription quantitative PCR with a κ coefficient of 0.979. Conclusions The mobile laboratory provides a promising solution for fast deployment of medical diagnostic resources at critical junctions of infectious disease outbreaks and facilitates local containment of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) transmission.

scholarly journals Rapid, accurate, nucleobase detection using FnCas9

2020 ◽  
Author(s):  
Mohd. Azhar ◽  
Rhythm Phutela ◽  
Manoj Kumar ◽  
Asgar Hussain Ansari ◽  
Riya Rauthan ◽  
...  
Keyword(s):  
Point Of Care ◽  
Disease Outbreaks ◽  
Smartphone Application ◽  
Clinical Samples ◽  
Single Nucleotide Variants ◽  
Clinical Prognosis ◽  
Viral Loads ◽  
Infectious Disease Outbreaks ◽  
Dna And Rna ◽  
True Outcome

Rapid detection of pathogenic sequences or variants in DNA and RNA through a point-of-care diagnostic approach is valuable for accelerated clinical prognosis as has been witnessed during the recent COVID-19 outbreak. Traditional methods relying on qPCR or sequencing are difficult to implement in settings with limited resources necessitating the development of accurate alternative testing strategies that perform robustly. Here, we present FnCas9 Editor Linked Uniform Detection Assay (FELUDA) that employs a direct Cas9 based enzymatic readout for detecting nucleotide sequences and identifying nucleobase identity without the requirement of trans-cleavage activity of reporter molecules. We demonstrate that FELUDA is 100% accurate in detecting single nucleotide variants (SNVs) including heterozygous carriers of a mutation and present a simple design strategy in the form of a web-tool, JATAYU, for its implementation. FELUDA is semi quantitative, can be adapted to multiple signal detection platforms and can be quickly designed and deployed for versatile applications such as infectious disease outbreaks like COVID-19. Using a lateral flow readout within 1h, FELUDA shows 100% sensitivity and 97% specificity across all range of viral loads in clinical samples. In combination with RT-RPA and a smartphone application True Outcome Predicted via Strip Evaluation (TOPSE), we present a prototype for FELUDA for CoV-2 detection at home.

scholarly journals Efficacy of Mass Quarantine as Leverage of Health System Governance During COVID-19 Outbreak: A Mini Policy Review

2020 ◽  
Vol 23 (4) ◽  
pp. 265-267 ◽  
Author(s):  
Mohammad Hossein Taghrir ◽  
Hossein Akbarialiabad ◽  
Milad Ahmadi Marzaleh
Keyword(s):  
Health System ◽  
Disease Outbreaks ◽  
Chinese Government ◽  
The Public ◽  
Infectious Disease Outbreaks ◽  
Course Of Action ◽  
Health System Governance ◽  
The Impact ◽  
The City ◽  
Health Policymaking

On January 23, 2020, the Chinese government announced the city lockdown of Wuhan. Since then, there have been controversial debates among experts about the efficacy of mass quarantine, the oldest and probably one of the most effective methods for controlling infectious disease outbreaks. The impact of health policymaking section of health system governance becomes visible to all stakeholders and the public in such emergency contexts. The success and failure of such policies should be evaluated in order to find the proper course of action for the local and international communities. In this review, we aim to investigate the efficacy of mass quarantine in China during the coronavirus disease 2019 (COVID-19) pandemic. We found good quality evidence for the effectiveness of mass quarantine during the current stage of COVID-19 pandemic, and these strategies seem to have been highly effective in controlling the spread of the disease.

scholarly journals Wastewater treatment in the city of Koprivnica

2020 ◽  
Vol 12 (2) ◽  
pp. 296-306
Author(s):  
Anita Ptiček Siročić ◽  
Ivana Mlinarić ◽  
Dragana Dogančić ◽  
Nikola Sakač ◽  
Sanja Horvat
Keyword(s):  
Wastewater Treatment ◽  
Wastewater Treatment Plants ◽  
Batch Reactor ◽  
Treatment Plant ◽  
Oxygen Demand ◽  
Natural State ◽  
Primary Role ◽  
Wastewater Quality ◽  
Wastewater Samples ◽  
The City

Basedon the concept of sustainable development, water must be stored and protected for present and future generations. This also means saving the water through wastewater treatment. The primary role of the wastewater treatment plants is to treat wastewaters upto a satisfactory level of quality as close as possible to the natural state. The central wastewater treatment plant (WWTP) of the City of Koprivnica treats wastewater including the tertiary wastewater. Due to considerable fluctuations in wastewater volumes and loads, sequential batch reactor (SBR) technology was selected as the best solution for wastewater treatment. The final stage of treatment at the WWTP of the City of Koprivnica is the process of sludge treatment by aerobic stabilization, dehydration and MID-MIX technology, which produces a chemicallyinert powder –solidificate. Solidificate can be used in civil engineering or it can be disposed tolandfill without environmental impact. This paper analyses the physical-chemical indicators of wastewater quality (chemical oxygen demand -COD, biological oxygen demand -BOD5, total nitrogen, total phosphorus, suspended matter) on wastewater samples from the WWTP of the City of Koprivnica in a period from 2014 to 2016. The results indicate that the treatedwastewater has a satisfactory quality and that the WWTP of the City of Koprivnica works efficiently.

Leading the City of Baltimore into the 21st Century: Flexible Treatment Solutions and Integrated Raw Water Management

2010 ◽  
Vol 5 (4) ◽  
Author(s):  
J. L. Manuszak ◽  
M. MacPhee ◽  
S. Liskovich ◽  
L. Feldsher
Keyword(s):  
Water Management ◽  
Water Quality ◽  
Water Supply ◽  
Conceptual Design ◽  
Membrane Filtration ◽  
Treatment Plant ◽  
Low Pressure ◽  
Management Tool ◽  
Raw Water ◽  
The City

The City of Baltimore, Maryland is one of many US cities faced with challenges related to increasing potable water demands, diminishing fresh water supplies, and aging infrastructure. To address these challenges, the City recently undertook a $7M study to evaluate water supply and treatment alternatives and develop the conceptual design for a new 120 million gallon per day (MGD) water treatment plant. As part of this study, an innovative raw water management tool was constructed to help model source water availability and predicted water quality based on integration of a new and more challenging surface water supply. A rigorous decision-making approach was then used to screen and select appropriate treatment processes. Short-listed treatment strategies were demonstrated through a year-long pilot study, and process design criteria were collected in order to assess capital and operational costs for the full-scale plant. Ultimately the City chose a treatment scheme that includes low-pressure membrane filtration and post-filter GAC adsorption, allowing for consistent finished water quality irrespective of which raw water supply is being used. The conceptual design includes several progressive concepts, which will: 1) alleviate treatment limitations at the City's existing plants by providing additional pre-clarification facilities at the new plant; and 2) take advantage of site conditions to design and operate the submerged membrane system by gravity-induced siphon, saving the City significant capital and operations and maintenance (O&M) costs. Once completed, the new Fullerton Water Filtration Plant (WFP) will be the largest low-pressure membrane plant in North America, and the largest gravity-siphon design in the world.

The Implementation of Biological Phosphorus and Nitrogen Removal with the Bio-Denipho Process on a 265,000 PE Treatment Plant

1992 ◽  
Vol 25 (4-5) ◽  
pp. 161-168 ◽  
Author(s):  
J. Einfeldt
Keyword(s):  
Nitrogen Removal ◽  
Treatment Plant ◽  
First Year ◽  
In Series ◽  
Design Loads ◽  
Last Stage ◽  
Two Stages ◽  
The City ◽  
Biological Phosphorus

A process, called Bio-Denipho, for combined biological phosphorus and nitrogen removal in a combination of an anaerobic tank and two oxidation ditches is described. In this process the anaerobic tank consisting of three sections working in series is followed by two oxidation ditches. These too are working in series, but with both inlet to and outlet from the tanks changing in a cycle. The Bio-Denipho process is described specifically for the process itself and as a case study for the implementation of the process on a 265,000 pe wastewater treatment plant for the city of Aalborg in Denmark. The plant was designed and erected in two stages and the last stage was inaugurated October 31,1989. Lay-out and functions for the plant is described and design loads, plan lay-out and tank volumes are given in this paper together with performance data for the first year in operation.

Two-stage chemical-biological treatment at Thessaloniki greater area WWTP - experiences and potentials

1995 ◽  
Vol 32 (9-10) ◽  
pp. 75-84 ◽  
Author(s):  
A. D. Andreadakis ◽  
G. H. Kristensen ◽  
A. Papadopoulos ◽  
C. Oikonomopoulos
Keyword(s):  
Biological Treatment ◽  
Treatment Plant ◽  
Cost Effective ◽  
Primary Treatment ◽  
Effective Control ◽  
Two Stage ◽  
Effluent Quality ◽  
Filamentous Microorganisms ◽  
Sludge Settling ◽  
The City

The wastewater from the city of Thessaloniki is discharged without treatment to the nearby inner part of the Thessaloniki Gulf. The existing, since 1989, treatment plant offers only primary treatment and did not operate since the expected effluent quality is not suitable for safe disposal to the available recipients. Upgrading of the plant for advanced biological treatment, including seasonal nitrogen removal, is due from 1995. In the mean time, after minor modifications completed in February 1992, the existing plant was put into operation as a two-stage chemical-biological treatment plant for 40 000 m3 d−1, which corresponds to about 35% of the total sewage flow. The operational results obtained during the two years operation period are presented and evaluated. All sewage and sludge treatment units of the plant perform better than expected, with the exception of the poor sludge settling characteristics, due to severe and persistent bulking caused by excessive growth of filamentous microorganisms, particularly M. Parvicella. Effective control of the bulking problem could lead to more cost-effective operation and increased influent flows.

scholarly journals Infectious disease outbreaks in the African region: overview of events reported to the World Health Organization in 2018

2019 ◽  
Vol 147 ◽  
Author(s):  
F. Mboussou ◽  
P. Ndumbi ◽  
R. Ngom ◽  
Z. Kassamali ◽  
O. Ogundiran ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Disease Onset ◽  
Disease Outbreaks ◽  
Case Fatality ◽  
World Health ◽  
African Region ◽  
Regional Office ◽  
Member States ◽  
Infectious Disease Outbreaks ◽  
The World

Abstract The WHO African region is characterised by the largest infectious disease burden in the world. We conducted a retrospective descriptive analysis using records of all infectious disease outbreaks formally reported to the WHO in 2018 by Member States of the African region. We analysed the spatio-temporal distribution, the notification delay as well as the morbidity and mortality associated with these outbreaks. In 2018, 96 new disease outbreaks were reported across 36 of the 47 Member States. The most commonly reported disease outbreak was cholera which accounted for 20.8% (n = 20) of all events, followed by measles (n = 11, 11.5%) and Yellow fever (n = 7, 7.3%). About a quarter of the outbreaks (n = 23) were reported following signals detected through media monitoring conducted at the WHO regional office for Africa. The median delay between the disease onset and WHO notification was 16 days (range: 0–184). A total of 107 167 people were directly affected including 1221 deaths (mean case fatality ratio (CFR): 1.14% (95% confidence interval (CI) 1.07%–1.20%)). The highest CFR was observed for diseases targeted for eradication or elimination: 3.45% (95% CI 0.89%–10.45%). The African region remains prone to outbreaks of infectious diseases. It is therefore critical that Member States improve their capacities to rapidly detect, report and respond to public health events.

scholarly journals Assessment of Microplastics in a Municipal Wastewater Treatment Plant with Tertiary Treatment: Removal Efficiencies and Loading per Day into the Environment

Water ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 1339
Author(s):  
Javier Bayo ◽  
Sonia Olmos ◽  
Joaquín López-Castellanos
Keyword(s):  
Wastewater Treatment ◽  
Wastewater Treatment Plant ◽  
Municipal Wastewater ◽  
Removal Rate ◽  
Treatment Plant ◽  
Source Control ◽  
Municipal Wastewater Treatment ◽  
Tertiary Treatment ◽  
Stable Performance ◽  
Wastewater Samples

This study investigates the removal of microplastics from wastewater in an urban wastewater treatment plant located in Southeast Spain, including an oxidation ditch, rapid sand filtration, and ultraviolet disinfection. A total of 146.73 L of wastewater samples from influent and effluent were processed, following a density separation methodology, visual classification under a stereomicroscope, and FTIR analysis for polymer identification. Microplastics proved to be 72.41% of total microparticles collected, with a global removal rate of 64.26% after the tertiary treatment and within the average retention for European WWTPs. Three different shapes were identified: i.e., microfiber (79.65%), film (11.26%), and fragment (9.09%), without the identification of microbeads despite the proximity to a plastic compounding factory. Fibers were less efficiently removed (56.16%) than particulate microplastics (90.03%), suggesting that tertiary treatments clearly discriminate between forms, and reporting a daily emission of 1.6 × 107 microplastics to the environment. Year variability in microplastic burden was cushioned at the effluent, reporting a stable performance of the sewage plant. Eight different polymer families were identified, LDPE film being the most abundant form, with 10 different colors and sizes mainly between 1–2 mm. Future efforts should be dedicated to source control, plastic waste management, improvement of legislation, and specific microplastic-targeted treatment units, especially for microfiber removal.

scholarly journals Antimicrobial Activity of Chitosan Oligosaccharides with Special Attention to Antiparasitic Potential

Marine Drugs ◽  
2021 ◽  
Vol 19 (2) ◽  
pp. 110
Author(s):  
Nayara Sousa da Silva ◽  
Nathália Kelly Araújo ◽  
Alessandra Daniele-Silva ◽  
Johny Wysllas de Freitas Oliveira ◽  
Júlia Maria de Medeiros ◽  
...  
Keyword(s):  
Disease Outbreaks ◽  
Biological Properties ◽  
Enzymatic Production ◽  
Infectious Disease Outbreaks ◽  
Chitosan Oligosaccharides ◽  
Lower Viscosity ◽  
Biomedical Industry ◽  
Parasite Aggregation ◽  
Hydrolysis Of

The global rise of infectious disease outbreaks and the progression of microbial resistance reinforce the importance of researching new biomolecules. Obtained from the hydrolysis of chitosan, chitooligosaccharides (COSs) have demonstrated several biological properties, including antimicrobial, and greater advantage over chitosan due to their higher solubility and lower viscosity. Despite the evidence of the biotechnological potential of COSs, their effects on trypanosomatids are still scarce. The objectives of this study were the enzymatic production, characterization, and in vitro evaluation of the cytotoxic, antibacterial, antifungal, and antiparasitic effects of COSs. NMR and mass spectrometry analyses indicated the presence of a mixture with 81% deacetylated COS and acetylated hexamers. COSs demonstrated no evidence of cytotoxicity upon 2 mg/mL. In addition, COSs showed interesting activity against bacteria and yeasts and a time-dependent parasitic inhibition. Scanning electron microscopy images indicated a parasite aggregation ability of COSs. Thus, the broad biological effect of COSs makes them a promising molecule for the biomedical industry.

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