Detection of enterovirus in environmental waters: A new optimized method compared to commercial real-time RT-qPCR kits

Wurtzer, Sébastien; Prévost, Benoit; Lucas, Françoise; Moulin, Laurent

doi:10.1016/j.jviromet.2014.08.016

Cited by 23 publications

(9 citation statements)

References 29 publications

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“…An internal positive control (IPC) was added to evaluate the presence of residual inhibitors. The IPC consists in a plasmid-containing, beta-acting gene flanked by enterovirus-specific primers [29]. The detection limit was estimated to be around 10 3 genome units per liter (GU/L) of raw WW.…”

Section: Molecular Detection Methodsmentioning

confidence: 99%

Evaluation of lockdown effect on SARS-CoV-2 dynamics through viral genome quantification in waste water, Greater Paris, France, 5 March to 23 April 2020

et al. 2020

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Introduction Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of coronavirus disease (COVID-19). People infected with SARS-CoV-2 may exhibit no or mild non-specific symptoms; thus, they may contribute to silent circulation of the virus among humans. Since SARS-CoV-2 RNA can be detected in stool samples, monitoring SARS-CoV-2 RNA in waste water (WW) has been proposed as a complementary tool to investigate virus circulation in human populations. Aim To test if the quantification of SARS-CoV-2 genomes in WW correlates with the number of symptomatic or non-symptomatic carriers. Method We performed a time-course quantitative analysis of SARS-CoV-2 by RT-qPCR in raw WW samples collected from several major WW treatment plants in Greater Paris. The study period was 5 March to 23 April 2020, including the lockdown period in France (from 17 March). Results We showed that the increase of genome units in raw WW accurately followed the increase of human COVID-19 cases observed at the regional level. Of note, the viral genome could be detected before the epidemic grew massively (around 8 March). Equally importantly, a marked decrease in the quantities of genome units was observed concomitantly with the reduction in the number of new COVID-19 cases, 29 days following the lockdown. Conclusion This work suggests that a quantitative monitoring of SARS-CoV-2 genomes in WW could generate important additional information for improved monitoring of SARS-CoV-2 circulation at local or regional levels and emphasises the role of WW-based epidemiology.

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Section: Molecular Detection Methodsmentioning

confidence: 99%

Evaluation of lockdown effect on SARS-CoV-2 dynamics through viral genome quantification in waste water, Greater Paris, France, 5 March to 23 April 2020

et al. 2020

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“…Effluent samples were concentrated by three successive filtration/concentration steps as described previously (13). Briefly, 10 liters of sample was filtered using electropositive filters (NanoCeram virus samplers; Argonide, Sanford, FL).…”

Section: Methodsmentioning

confidence: 99%

Deciphering the Diversities of Astroviruses and Noroviruses in Wastewater Treatment Plant Effluents by a High-Throughput Sequencing Method

Prévost

Lucas

Ambert-Balay³

et al. 2015

Appl Environ Microbiol

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cAlthough clinical epidemiology lists human enteric viruses to be among the primary causes of acute gastroenteritis in the human population, their circulation in the environment remains poorly investigated. These viruses are excreted by the human population into sewers and may be released into rivers through the effluents of wastewater treatment plants (WWTPs). In order to evaluate the viral diversity and loads in WWTP effluents of the Paris, France, urban area, which includes about 9 million inhabitants (approximately 15% of the French population), the seasonal occurrence of astroviruses and noroviruses in 100 WWTP effluent samples was investigated over 1 year. The coupling of these measurements with a high-throughput sequencing approach allowed the specific estimation of the diversity of human astroviruses (human astrovirus genotype 1 [HAstV-1], HAstV-2, HAstV-5, and HAstV-6), 7 genotypes of noroviruses (NoVs) of genogroup I (NoV GI.1 to NoV GI.6 and NoV GI.8), and 16 genotypes of NoVs of genogroup II (NoV GII.1 to NoV GII.7, NoV GII.9, NoV GII.12 to NoV GII.17, NoV GII.20, and NoV GII.21) in effluent samples. Comparison of the viral diversity in WWTP effluents to the viral diversity found by analysis of clinical data obtained throughout France underlined the consistency between the identified genotypes. However, some genotypes were locally present in effluents and were not found in the analysis of the clinical data. These findings could highlight an underestimation of the diversity of enteric viruses circulating in the human population. Consequently, analysis of WWTP effluents could allow the exploration of viral diversity not only in environmental waters but also in a human population linked to a sewerage network in order to better comprehend viral epidemiology and to forecast seasonal outbreaks.T he epidemiology of viral gastroenteritis is mainly evaluated through the use of clinical data. However, clinical data provide only a partial vision of the gastroenteritis viruses circulating in the human population. Indeed, many viral infections do not require specialized consultations or hospitalizations and so are not directly included in clinical statistics. As a consequence, these data sets offer a limited view of the diversity and occurrence of enteric viruses in the human population.Human astroviruses (HAstVs) and noroviruses (NoVs) are among the main causes of human acute gastroenteritis worldwide (1, 2). HAstVs and NoVs are nonenveloped viruses and have a positive-sense single-stranded RNA. The genome of HAstV is composed of three open reading frames (ORFs), and ORF2, encoding the capsid protein precursor, allows discrimination of eight genotypes of HAstV, HAstV-1 to HAstV-8 (3). The genome of NoV is also composed of three ORFs, and genotyping based on the genetic similarity of ORF2 and ORF3 allows discrimination of 9 genotypes of NoV genogroup I (NoV GI) and 22 genotypes of NoV genogroup II (NoV GII), which are the most common genogroups associated with human infections.HAstVs and NoVs are able to infect i...

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“…An internal positive control (IPC) was added to evaluate the presence of residual inhibitors. The IPC consists in a plasmid containing beta-acting gene flanked by enterovirus-specific primers (Wurtzer et al, 2014). The detection limit was estimated to be around 10 genome units per amplification reaction.…”

Section: Viral Rna Titrationmentioning

confidence: 99%

Several forms of SARS-CoV-2 RNA can be detected in wastewaters : implication for wastewater-based epidemiology and risk assessment

Wurtzer

Waldman

Ferrier-Rembert³

et al. 2020

Preprint

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The ongoing global pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a public health emergency of international concern. Although SARS-CoV-2 is considered to be mainly transmitted by inhalation of contaminated droplets and aerosols, SARS-CoV-2 is also detected in human feces and in raw wastewaters suggesting that other routes of infection may exist. Monitoring SARS-CoV-2 genomes in wastewaters has been proposed as a complementary approach for tracing the dynamics of virus transmission within human population connected to wastewater network. The understanding on SARS-CoV-2 transmission through wastewater surveillance, the development of epidemic modeling and the evaluation of SARS-CoV-2 transmission from contaminated wastewater are largely limited by our knowledge on viral RNA genome persistence and virus infectivity preservation in such an environment. Using an integrity based RT-qPCR assay this study led to the discovery that SARS-CoV-2 RNA can persist under several forms in wastewaters, which provides important information on the presence of SARS-CoV-2 in raw wastewaters and associated risk assessment.Graphical Abstract

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Detection of enterovirus in environmental waters: A new optimized method compared to commercial real-time RT-qPCR kits

Cited by 23 publications

References 29 publications

Evaluation of lockdown effect on SARS-CoV-2 dynamics through viral genome quantification in waste water, Greater Paris, France, 5 March to 23 April 2020

Evaluation of lockdown effect on SARS-CoV-2 dynamics through viral genome quantification in waste water, Greater Paris, France, 5 March to 23 April 2020

Deciphering the Diversities of Astroviruses and Noroviruses in Wastewater Treatment Plant Effluents by a High-Throughput Sequencing Method

Several forms of SARS-CoV-2 RNA can be detected in wastewaters : implication for wastewater-based epidemiology and risk assessment

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