scholarly journals The Rapid Assessment of Aggregated Wastewater Samples for Genomic Surveillance of SARS-CoV-2 on a City-Wide Scale

Pathogens ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1271
Author(s):  
Eric C. Rouchka ◽  
Julia H. Chariker ◽  
Kumar Saurabh ◽  
Sabine Waigel ◽  
Wolfgang Zacharias ◽  
...  
Keyword(s):  
Public Health ◽  
Next Generation Sequencing ◽  
Rapid Assessment ◽  
Wastewater Management ◽  
Next Generation ◽  
Catchment Areas ◽  
Neighborhood Scale ◽  
Wastewater Samples ◽  
The Individual ◽  
Generation Sequencing

Throughout the course of the ongoing SARS-CoV-2 pandemic there has been a need for approaches that enable rapid monitoring of public health using an unbiased and minimally invasive means. A major way this has been accomplished is through the regular assessment of wastewater samples by qRT-PCR to detect the prevalence of viral nucleic acid with respect to time and location. Further expansion of SARS-CoV-2 wastewater monitoring efforts to include the detection of variants of interest/concern through next-generation sequencing has enhanced the understanding of the SARS-CoV-2 outbreak. In this report, we detail the results of a collaborative effort between public health and metropolitan wastewater management authorities and the University of Louisville to monitor the SARS-CoV-2 pandemic through the monitoring of aggregate wastewater samples over a period of 28 weeks. Through the use of next-generation sequencing approaches the polymorphism signatures of Variants of Concern / Interest were evaluated to determine the likelihood of their prevalence within the community on the basis of their relative dominance within sequence datasets. Our data indicate that wastewater monitoring of water quality treatment centers and smaller neighborhood-scale catchment areas is a viable means by which the prevalence and genetic variation of SARS-CoV-2 within a metropolitan community of approximately one million individuals may be monitored, as our efforts detected the introduction and emergence of variants of concern in the city of Louisville. Importantly, these efforts confirm that regional emergence and spread of variants of interest/concern may be detected as readily in aggregate wastewater samples as compared to the individual wastewater sheds. Furthermore, the information gained from these efforts enabled targeted public health efforts including increased outreach to at-risk communities and the deployment of mobile or community-focused vaccination campaigns.

scholarly journals The Rapid Assessment of Aggregated Wastewater Samples for Genomic Surveillance of SARS-CoV-2 on a City-Wide Scale

2021 ◽  
Author(s):  
Eric C. Rouchka ◽  
Julia L. Chariker ◽  
Kumar Saurabh ◽  
Sabine Waigel ◽  
Wolfgang Zacharias ◽  
...  
Keyword(s):  
Public Health ◽  
Rapid Assessment ◽  
Wastewater Management ◽  
Catchment Areas ◽  
University Of Louisville ◽  
Rapid Monitoring ◽  
Wide Scale ◽  
Neighborhood Scale ◽  
Wastewater Samples ◽  
The Individual

AbstractThroughout the course of the ongoing SARS-CoV-2 pandemic there has been a need for approaches that enable rapid monitoring of public health using an unbiased and minimally invasive means. A major way this has been accomplished is through the regular assessment of wastewater samples by qRT-PCR to detect the prevalence of viral nucleic acid with respect to time and location. Further expansion of SARS-CoV-2 wastewater monitoring efforts to include the detection of variants of interest / concern through next-generation sequencing have enhanced the understanding of the SARS-CoV-2 outbreak. In this report we detail the results of a collaborative effort between public health and metropolitan wastewater management authorities and the University of Louisville to monitor the SARS-CoV-2 pandemic through the monitoring of aggregate wastewater samples over a period of 28 weeks. Our data indicates that wastewater monitoring of water quality treatment centers and smaller neighborhood-scale catchment areas is a viable means by which the prevalence and genetic variation of SARS-CoV-2 within a metropolitan community of approximately one million individuals may be monitored. Importantly, these efforts confirm that regional emergence and spread of variants of interest / concern may be detected as readily in aggregate wastewater samples as compared to the individual wastewater sheds.

scholarly journals Environmental Surveillance through Next-Generation Sequencing to Unveil the Diversity of Human Enteroviruses beyond the Reported Clinical Cases

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 120
Author(s):  
Andrés Lizasoain ◽  
Daiana Mir ◽  
Gisella Masachessi ◽  
Adrián Farías ◽  
Nélida Rodríguez-Osorio ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Echovirus 30 ◽  
Coxsackievirus B4 ◽  
Important Region ◽  
Enterovirus A71 ◽  
Wastewater Samples ◽  
Valuable Role ◽  
Generation Sequencing

The knowledge about circulation of Human Enteroviruses (EVs) obtained through medical diagnosis in Argentina is scarce. Wastewater samples monthly collected in Córdoba, Argentina during 2011–2012, and then in 2017–2018 were retrospectively studied to assess the diversity of EVs in the community. Partial VP1 gene was amplified by PCR from wastewater concentrates, and amplicons were subject of next-generation sequencing and genetic analyses. There were 41 EVs detected, from which ~50% had not been previously reported in Argentina. Most of the characterized EVs (60%) were detected at both sampling periods, with similar values of intratype nucleotide diversity. Exceptions were enterovirus A71, coxsackievirus B4, echovirus 14, and echovirus 30, which diversified in 2017–2018. There was a predominance of types from EV-C in 2017–2018, evidencing a common circulation of these types throughout the year in the community. Interestingly, high genetic similarity was evidenced among environmental strains of echovirus 30 circulating in 2011–2012 and co-temporal isolates obtained from patients suffering aseptic meningitis in different locations of Argentina. This study provides an updated insight about EVs circulating in an important region of South America, and suggests a valuable role of wastewater-based epidemiology in predicting outbreaks before the onset of cases in the community.

scholarly journals Practical Guidance to Implementing Quality Management Systems in Public Health Laboratories Performing Next-Generation Sequencing: Personnel, Equipment, and Process Management (Phase 1)

2019 ◽  
Vol 57 (8) ◽  
Author(s):  
Rebecca J. Hutchins ◽  
Kristy L. Phan ◽  
Adeeba Saboor ◽  
Joseph D. Miller ◽  
Atis Muehlenbachs
Keyword(s):  
Public Health ◽  
Next Generation Sequencing ◽  
Quality Management ◽  
Process Management ◽  
Quality Management System ◽  
Phase 1 ◽  
Quality System ◽  
Clinical Diagnostics ◽  
Next Generation ◽  
Generation Sequencing

ABSTRACT Quality standards as part of an effective quality management system (QMS) are the cornerstone for generating high-quality test results. Next-generation sequencing (NGS) has the potential to improve both clinical diagnostics and public health surveillance efforts in multiple areas, including infectious diseases. However, the laboratories adopting NGS methods face significant challenges due to the complex and modular process design. This document summarizes the first phase of quality system guidance developed by the Centers for Disease Control and Prevention (CDC) NGS Quality Workgroup. The quality system essentials of personnel, equipment, and process management (quality control and validation) were prioritized based on a risk assessment using information gathered from participating CDC laboratories. Here, we present a prioritized QMS framework, including procedures and documentation tools, to assist laboratory implementation and maintenance of quality practices for NGS workflows.

scholarly journals A platform for leveraging next generation sequencing for routine microbiology and public health use

2015 ◽  
Vol 3 (S1) ◽  
Author(s):  
Laura I Rusu ◽  
Kelly L Wyres ◽  
Matthias Reumann ◽  
Carlos Queiroz ◽  
Alexe Bojovschi ◽  
...  
Keyword(s):  
Public Health ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Next Generation Sequencing Identifies Five Major Classes of Potentially Therapeutic Enzymes Secreted byLucilia sericataMedical Maggots

2016 ◽  
Vol 2016 ◽  
pp. 1-27 ◽  
Author(s):  
Zdeněk Franta ◽  
Heiko Vogel ◽  
Rüdiger Lehmann ◽  
Oliver Rupp ◽  
Alexander Goesmann ◽  
...  
Keyword(s):  
Wound Healing ◽  
Next Generation Sequencing ◽  
Chronic Wounds ◽  
De Novo ◽  
Therapeutic Effects ◽  
Next Generation ◽  
Larval Body ◽  
Accelerate Wound Healing ◽  
The Individual ◽  
Generation Sequencing

Lucilia sericatalarvae are used as an alternative treatment for recalcitrant and chronic wounds. Their excretions/secretions contain molecules that facilitate tissue debridement, disinfect, or accelerate wound healing and have therefore been recognized as a potential source of novel therapeutic compounds. Among the substances present in excretions/secretions various peptidase activities promoting the wound healing processes have been detected but the peptidases responsible for these activities remain mostly unidentified. To explore these enzymes we applied next generation sequencing to analyze the transcriptomes of different maggot tissues (salivary glands, gut, and crop) associated with the production of excretions/secretions and/or with digestion as well as the rest of the larval body. As a result we obtained more than 123.8 million paired-end reads, which were assembledde novousing Trinity and Oases assemblers, yielding 41,421 contigs with an N50 contig length of 2.22 kb and a total length of 67.79 Mb. BLASTp analysis against the MEROPS database identified 1729 contigs in 577 clusters encoding five peptidase classes (serine, cysteine, aspartic, threonine, and metallopeptidases), which were assigned to 26 clans, 48 families, and 185 peptidase species. The individual enzymes were differentially expressed among maggot tissues and included peptidase activities related to the therapeutic effects of maggot excretions/secretions.

scholarly journals Alcov: Estimating Variant of Concern Abundance from SARS-CoV-2 Wastewater Sequencing Data

2021 ◽  
Author(s):  
Isaac Ellmen ◽  
Michael D.J. Lynch ◽  
Delaney Nash ◽  
Jiujun Cheng ◽  
Jozef I. Nissimov ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Data ◽  
Relative Abundance ◽  
Community Level ◽  
Next Generation ◽  
Sequencing Data ◽  
Complete Genomes ◽  
Relative Abundances ◽  
Wastewater Samples ◽  
Generation Sequencing

Detection of SARS-CoV-2 in wastewater is an important strategy for community level surveillance. Variants of concern (VOCs) can be detected in the wastewater samples using next generation sequencing, however it can be challenging to determine the relative abundance of different VOCs since the reads cannot be assembled into complete genomes. Here, we present Alcov (abundance learning of SARS-CoV-2 variants), a tool that uses mutation frequencies in SARS-CoV-2 sequencing data to predict the distribution of VOC lineages in the sample. We used Alcov to predict the distributions of lineages from three wastewater samples which agreed well with clinical data. By predicting not just which VOCs are present, but their relative abundances in the population, Alcov extracts a more complete snapshot of the variants which are circulating in a community.

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