ABSTRACT
Background: The quantification of SARS-CoV-2 in wastewater is a tool that allows determining the trend of viral circulation in a particular geographical area. Aim(s): To quantify the SARS-CoV-2 virus in 15 wastewater treatment plants in different Chilean cities to establish a comparison with the variables of: I) Active cases per 100,000 inhabitants;ii) daily positivity (novel cases);and iii) phases of the lockdown strategy. Method(s): SARS-CoV-2 was concentrated from wastewater samples. To obtain the number of virus genomes per liter, absolute quantification was performed using qRT-PCR. Result(s): Between January and June 2021, 253 samples were processed, all of which were positive for the presence of the virus. Likewise, it will be determined that the rate of active cases per 100,000 inhabitants is the variable that best fits the trends obtained with the quantification of the viral load in wastewater. Conclusion(s): The quantification of SARS- CoV-2 in wastewater as a continuous strategy is an efficient tool to determine the trend of the viral circulation in a delimited geographical area and, combined with genomic surveillance, it can constitute an ideal sentinel surveillance alert on future outbreaks.Copyright © 2022, Sociedad Chilena de Infectologia. All rights reserved.
ABSTRACT
Background: Wastewater represents a broad, immediate, and unbiased accounting of the pathgens in the population. We aimed to develop methods to track HIV in wastewater utilizing a viral detection pipeline adapted from platforms developed to track SARS-COV-2. Method(s): We used samples from 6 wastewater treatment plants in the Houston area. We focused on regions of higher prevalence and lower prevalence. First, employing wastewater processing and nucleic acid extraction methods described by our group to detect SARS-COV-2, we tested a single high and low prevalence site in triplicate with all 3 primer sets. nucleic acid extracts from HIV and SIV cell culture supernatants were used as controls. Next, in subsequent samples, RT-PCR reactions with detections were subjected to gel electrophoresis to determine the amplified product sizes. To further confirm HIV detection, we sequenced the RT-PCR products and compared the proportion of reads which mapped to the expected amplified product. In a later set of studies, we fractionated samples into supernatant and pellet. We further tested HIV presence by performing whole virome sequencing on the extracts from some samples that produced detections and mapped reads to published genomes. A crAssphage genome was used as a negative control. Result(s): Samples from all sites resulted in signal detection at least once. Only reactions with gag and pol primers appeared to amplify the expected product. Products from the HIV positive control mapped almost exclusively to the HIV genome (97-100% of reads), with a fraction of reads from the SIV negative control doing the same (16-18% of reads). The ltr and pol products did not map the HIV genome while gag products did (34-44% of reads). Among the fractionated sample, in total, 6 supernatant fractions produced no detection compared to 7 of 8 pellet fractions. The whole virome sequencing produced reads that mapped to the HIV genome with at least 8X depth coverage. The sample with the lowest Ct detection (26) yielded HIV coverage several logs greater than those samples with higher Ct detection (37). Reads from all samples mapped to at least 20% of the HIV genome. Conclusion(s): This work provides the first evidence that HIV can be detected in municipal wastewater systems and has the potential to be developed into a new public health tool.
ABSTRACT
Introduction/ Background: Findings from wastewater-based epidemiology (WBE) surveillance of SARS-CoV-2 are increasingly used to monitor the epidemiology of SARS-CoV-2. We report on the findings from the South African Collaboration COVID-19 Environmental Surveillance System (SACCESS) laboratories and compare these with clinically obtained data. Methods: Wastewater grab or passive samples and underwent concentration, RNA extraction, reverse-transcriptasepolymerase chain reaction (RT-PCR) detection and quantification of SARS-CoV-2. Following whole genome amplicon-based sequencing, nonsynonymous mutations in the spike protein specific to variants of concern (VOCs) were identified. Quantitative RNA concentrations in genome copies/mL and the read-frequencies of lineagespecific single nucleotide polymorphisms (SNPs) in the spike protein of SARS-CoV-2 were plotted alongside official case load and SARS-Cov-2 lineage distribution by epidemiological week (provided by NICD SARS-CoV-2 epidemiology team and the Centre for Respiratory Diseases and Meningitis of the NICD). Results: Results from 95 wastewater treatment plants (WWTPs) across 9 provinces and all eight metropolitan areas of South Africa were collected weekly, biweekly or monthly from June 2020-October 2021 illustrate that increases and decreases in SARSCoV- 2 concentrations at all sites corresponded to metro-specific timing of the peak and post-peak decline in clinical cases. Increases in SARS-CoV-2 concentrations consistently preceded increases in clinical cases. In 18 WWTPs genomic analysis detected SNPs corresponding to prevalent VOCs and documented the change from beta to delta variant over the third SARS-CoV-2 wave. Impact: Without sufficient evidence that WBE findings correspond with clinical epidemiology and genomic results, public health authorities are often reluctant to use these data to guide decision making. Our findings illustrated that WBE monitoring of SARS-CoV-2 and detection of SNPs specific to SARS-CoV-2 variants correspond with clinical epidemiology and genomic findings. Conclusion: Wastewater based epidemiology including genotyping should be integrated into SARS-CoV-2 surveillance networks to support decision-making regarding public health interventions to contain SARS-CoV-2. Additional analyses to support interpretation of quantitative and genomic results should be done.
ABSTRACT
Introduction: Many studies have shown the advantages of monitoring wastewater in the evaluation of microbiological pathogens circulating in the community. It was aimed to detect of SARS-CoV-2 RNA with a simple concentration method in wastewater in this study. Materials and Methods: In our study, 7 wastewater samples were investigated, which were collected from the Urban Wastewater Treatment Plant (WWTP) of Çorum, between October to November 2020. Sorbent bags were left in water for 24 hours. Then they were used to trap and concentrate the virus. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) RNA detected by using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays. Results: As a result, 3 of the 7 samples taken were positive for N and ORF1ab target gene regions. Conclusion: This is the first study reporting the detection of SARS-CoV-2 RNA in wastewater with different concentration and capture method.
ABSTRACT
Wastewater-based epidemiology is a widely used tool to detect prevalence of viruses in the population. In the current COVID-19 pandemic, many countries began to analyze the novel coronavirus in sewage samples, and it was found a reliable method to monitor the tendencies of COVID-19 infections in different areas. The viral titer was observed to increase 4-10 days earlier in wastewater than the number of clinical cases. Therefore, the method could be used for early prediction. The method development started in April 2020 at National Public Health Centre (NPHC). Various concentration (flocculation, ultrafiltration) and RNA isolation methods (commercial kits and classic precipitation methods) were compared. The flocculation method showed low recovery rate, while the quality of the ultrafiltration method depended strongly on the type of filter unit. For the national survey, a specially manufactured membrane was chosen, due to its good recovery and reliable availability. The results of nucleic acid isolation were similar with the different methods, a commercial kit (Zymo Research) recommended to feces and soil was chosen due to its higher inhibitor-removal ability. RNA concentration is quantified by quantitative RT-PCR (designed for the nucleocapsid protein 1 gene), similar to the method used for clinical diagnostics. Systematic wastewater sampling started in end of May in Budapest;the survey was extended to all county capitals by the beginning of July. The operators of the wastewater treatment plants (WWTP) from the raw sewage carry the sampling out weekly after the grid filter, and the samples are shipped to the laboratory within 24 hours. Most WWTP does not have composite auto-sampler;therefore, sampling is carried out in the peak-load in most places. The results are available in 36-72 hours and published to NPHC website within a week. A decreasing trend was observable in the data from the end of May to the beginning of June, in parallel with the decline of the first wave of the epidemic. After that, the concentration of SARS-CoV-2 stagnated at a low level until beginning of August. The increasing trend in the wastewater was followed by an increase of the confirmed COVID-19 cases approximately 2 weeks later. Data processing is still ongoing for better modeling of the correlation between clinical data and SARS-CoV-2 concentration in wastewater.