https://digital.csic.es/bitstream/10261/239339/1/preprints202104.0481.v1.pdf

Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance

Trabajo presentado en la 113th General Meeting of the American Society for Microbiology, celebrada en Denver, Estados Unidos, del 18 al 21 de mayo de 2013

Species concept for prokaryotes

Wastewater surveillance of SARS-CoV-2 across 40 U.S. states from February to June 2020.

Understanding and managing uncertainty and variability for wastewater monitoring beyond the pandemic: Lessons learned from the United Kingdom national COVID-19 surveillance programmes.

Background: The effective reproductive number, Re, is a critical indicator to monitor disease dynamics, inform regional and national policies, and estimate the effectiveness of interventions. It describes the average number of new infections caused by a single infectious person through time. To date, Re estimates are based on clinical data such as observed cases, hospitalizations, and/or deaths. These estimates are temporarily biased when clinical testing or reporting strategies change. Objectives: We show that the dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater can be used to estimate Re in near real time, independent of clinical data and without the associated biases. Methods: We collected longitudinal measurements of SARS-CoV-2 RNA in wastewater in Zurich, Switzerland, and San Jose, California, USA. We combined this data with information on the temporal dynamics of shedding (the shedding load distribution) to estimate a time series proportional to the daily COVID-19 infection incidence. We estimated a wastewater-based Re from this incidence. Results: The method to estimate Re from wastewater worked robustly on data from two different countries and two wastewater matrices. The resulting estimates were as similar to the Re estimates from case report data as Re estimates based on observed cases, hospitalizations, and deaths are among each other. We further provide details on the effect of sampling frequency and the shedding load distribution on the ability to infer Re. Discussion: To our knowledge, this is the first time Re has been estimated from wastewater. This method provides a low-cost, rapid, and independent way to inform SARS-CoV-2 monitoring during the ongoing pandemic and is applicable to future wastewater-based epidemiology targeting other pathogens. https://doi.org/10.1289/EHP10050 

Wastewater-Based Estimation of the Effective Reproductive Number of SARS-CoV-2

A year since the declaration of the global coronavirus disease 2019 (COVID-19) pandemic there have been over 110 million cases and 2.5 million deaths. Using methods to track community spread of other viruses such as poliovirus, environmental virologists and those in the wastewater based epidemiology (WBE) field quickly adapted their existing methods to detect SARS-CoV-2 RNA in wastewater. Unlike COVID-19 case and mortality data, there was not a global dashboard to track wastewater monitoring of SARS-CoV-2 RNA worldwide. This study describes the development of the "COVIDPoops19" dashboard to disseminate information regarding sites, universities, research institutions and private laboratories in countries that are involved in WBE for SARS-CoV-2. Methods to assemble the dashboard combined standard literature review, direct submissions, and daily, social media keyword searches. Over 200 universities, 1,000 sites, and 50 countries with 59 dashboards monitor wastewater for SARS-CoV-2 RNA. However, monitoring is inequitably distributed in high-income countries and data are not widely shared publicly or accessible to researchers to inform public health actions, meta-analysis, better coordinate, and determine equitable distribution of monitoring sites. For WBE to be used to its full potential during COVID-19 and beyond, show us the data.

/pdf/show-us-the-data-global-covid-19-wastewater-monitoring-2ikk8jg5xp.pdf

Show us the Data: Global COVID-19 Wastewater Monitoring Efforts, Equity, and Gaps

Tetrasphaera are an attractive putative group of polyphosphate accumulating organisms (PAOs) that may play an important role in the enhanced biological phosphorus removal (EBPR) process. Unlike conventional PAOs that mostly rely on volatile fatty acids (VFAs), Tetrasphaera can assimilate a wide range of carbon substrates including glucose and various amino acids (e.g., glycine, glutamate, and aspartate). In addition, they have the ability to produce VFAs. This functional versatility confers significant performance and economic benefits for its application in EBPR processes. However, before the wastewater industry can harness these benefits, fundamental knowledge of their taxonomy, classification and identification in EBPR and activated sludge systems must be understood. This review provides a summary of the polyphasic approach: use of phenotypic, genotypic, and chemotaxonomic methods for bacterial classification and its application in the classification of Tetrasphaera. A review of molecular tools currently used to identify Tetrasphaera in activated sludge systems is also provided. In addition, this review discusses how challenges with molecular tools limit our understanding and application of Tetrasphaera in EBPR processes.

Yihan Zhang

Papers

Show us the Data: Global COVID-19 Wastewater Monitoring Efforts, Equity, and Gaps

Identification and classification of the Tetrasphaera genus in enhanced biological phosphorus removal process: a review