Characterisation of the sewage virome: comparison of NGS tools and occurrence of significant pathogens

Martínez-Puchol, Sandra; Rusiñol, Marta; Fernández-Cassi, Xavier; Timoneda, Natàlia; Itarte, Marta; Andrés, Cristina; Antón, Andrés; Abril, Josep F.; Gironés, Rosina; Bofill-Mas, Sı́lvia

doi:10.1016/j.scitotenv.2020.136604

Cited by 76 publications

(102 citation statements)

References 43 publications

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“…In the present study, ultracentrifugation was selected as the concentration methodology since it was previously applied by our team successfully [18,22,24] and its performance showed to be comparable to other methods such as aluminium hydroxide adsorption-precipitation procedure [26]. Currently, RT-qPCR is the golden standard used to study viral loads [26,44,45] from sewage samples but next generation sequencing (NGS) methodologies have emerged strongly in the field in two modalities, sequencing the total virome with or without enrichment [46][47][48] and the NGS sequencing of PCR amplicons [49].…”

Section: Discussionmentioning

confidence: 99%

Epidemiological Surveillance of Norovirus and Rotavirus in Sewage (2016–2017) in Valencia (Spain)

Santiso-Bellón,

Randazzo,

Pérez-Cataluña

et al. 2020

Microorganisms

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The aim of the present study was to perform the molecular epidemiology of rotaviruses and noroviruses detected in sewage samples from a large wastewater facility from the city of Valencia, Spain. A total of 46 sewage samples were collected over a one-year period (September 2016 to September 2017). Norovirus and rotavirus were detected and quantified by RT-qPCR, genotyped by semi-nested RT-PCR and further characterized by sequencing and phylogenetic analyses. Noroviruses and rotaviruses were widely distributed in sewage samples (69.6% for norovirus GI, 76.0% norovirus GII, and 71.7% rotaviruses) and viral loads varied from 4.33 to 5.75 log PCRU/L for norovirus GI, 4.69 to 6.95 log PCRU/L for norovirus GII, and 4.08 to 6.92 log PCRU/L for rotavirus. Overall, 87.5% (28/32) of GI noroviruses could not be genotyped, 6.25% (2/32) of the samples contained GI.2 genotype, and another 6.25% (2/32) were positive for GI.4 genotype. The most common genotype of GII noroviruses was GII.2 (40%, 14/35), followed by GII.6 (8.6%, 3/35) and GII.17 (5.7%, 2/35) while the remaining GII strains could not be typed (45.7%, 16/35). Rotavirus VP4 genotype P[8] was the only one found in 19 out of 33 rotavirus-positive samples (57.7%). G2 was the most prevalent rotavirus VP7 genotype (15.2%, 5/33) followed by G3, G9, and G12, with two positive samples for each genotype (6.1%, 2/33). In one sample both G1 and G2 genotypes were detected simultaneously (3%). The results presented here show that the surveillance of noroviruses and rotaviruses in sewage is useful for the study of their transmission in the population and their molecular epidemiology.

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Section: Discussionmentioning

confidence: 99%

Epidemiological Surveillance of Norovirus and Rotavirus in Sewage (2016–2017) in Valencia (Spain)

Santiso-Bellón,

Randazzo,

Pérez-Cataluña

et al. 2020

Microorganisms

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“…High-throughput sequencing has been recently applied in studies investigating the prevalence and diversity of viruses in sewage samples. The Next Generation Sequencing (NGS) technique allows a larger number of samples to be analyzed in a single run ( Hoy, 2019 ; Martínez-Puchol et al, 2020 ). In this type of sequencing, the following steps are involved: producing millions of copies of DNA fragments, and conducting and recording millions of sequences simultaneously ( Clark et al, 2019 ; Hoy, 2019 ).…”

Section: Detection Methods Of Viruses In Wastewatermentioning

confidence: 99%

“…In this type of sequencing, the following steps are involved: producing millions of copies of DNA fragments, and conducting and recording millions of sequences simultaneously ( Clark et al, 2019 ; Hoy, 2019 ). This parallel sequencing of a large number of samples reduces turnaround time and cost of sequencing ( Hoy, 2019 ; Martínez-Puchol et al, 2020 ).…”

Section: Detection Methods Of Viruses In Wastewatermentioning

confidence: 99%

“…NGS techniques were used by Martínez-Puchol et al (2020) to determine the distribution of human pathogenic viruses in three wastewater treatment plants in Barcelona City, Spain. Sequencing analyses showed that the three wastewater treatment plants had similar distribution of types of HAdV, HPV and HEV types despite the differences in the location, and volume of wastewater treated.…”

Section: Detection Methods Of Viruses In Wastewatermentioning

confidence: 99%

See 1 more Smart Citation

Viruses in wastewater: occurrence, abundance and detection methods

Corpuz

Buonerba

Vigliottá

et al. 2020

Science of The Total Environment

219

178

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This paper presents an updated and comprehensive review on the different methods used for detection and quantification of viruses in wastewater treatment systems. The analysis of viability of viruses in wastewater and sludge is another thrust of this review. Recent studies have mostly focused on determining the abundance and diversity of viruses in wastewater influents, in samples from primary, secondary, and tertiary treatment stages, and in final effluents. A few studies have also examined the occurrence and diversity of viruses in raw and digested sludge samples. Recent efforts to improve efficiency of virus detection and quantification methods in the complex wastewater and sludge matrices are highlighted in this review. A summary and a detailed comparison of the pre-treatment methods that have been utilized for wastewater and sludge samples are also presented. The role of metagenomics or sequencing analysis in monitoring wastewater systems to predict disease outbreaks, to conduct public health surveillance, to assess the efficiency of existing treatment systems in virus removal, and to re-evaluate current regulations regarding pathogenic viruses in wastewater is discussed in this paper. Challenges and future perspectives in the detection of viruses, including emerging and newly emerged viruses such as the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), in wastewater systems are discussed in this review.

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“…In addition, we could highlight selected references dealing with other viruses in sewage sludge, namely the papers by Bibby and Peccia (2013) , Nag et al (2020) and Martínez-Puchol et al (2020) , as well as other references for papers focusing on viruses in soils, specifically Kimura et al (2008) , Gutiérrez and Buchy (2012) (dealing with epidemic viruses), Williamson et al (2017) , and Kuzyakov and Mason-Jones (2018) . These papers would be an additional aid for those researchers trying to develop specific methods for SARS-Cov-2 and/or related viruses in samples from soil environments.…”

Section: Perspective and Discussionmentioning

confidence: 99%