Metagenomics for the study of viruses in urban sewage as a tool for public health surveillance

Fernández-Cassi, Xavier; Timoneda, Natàlia; Martínez-Puchol, Sandra; Rusiñol, Marta; Rodríguez-Manzano, Jesús; Figuerola, N; Bofill-Mas, Sı́lvia; Abril, Josep F.; Gironés, Rosina

doi:10.1016/j.scitotenv.2017.08.249

Cited by 142 publications

(128 citation statements)

References 87 publications

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“…There were different HAdV-F40 and HAdV-F41 strains in all inlet sewage samples, while in one ozone-treated sample a divergent type F strain dominated and in some of the treated waters there were type A strains. A somewhat similar finding was also obtained by Fernandez-Cassi and co-workers (Fernandez-Cassi et al, 2017). The pattern observed in this study suggests that there was a complex composition comprising multiple adenovirus types in the raw sewage, and these might have varying degrees of sensitivity to the conventional processing and ozone treatment.…”

Section: Discussionsupporting

confidence: 91%

Differential removal of human pathogenic viruses from sewage by conventional and ozone treatments

Wang

Sikora

Rutgersson

et al. 2018

International Journal of Hygiene and Environmental Health

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Sewage contains a mixed ecosystem of diverse sets of microorganisms, including human pathogenic viruses. Little is known about how conventional as well as advanced treatments of sewage, such as ozonation, reduce the environmental spread of viruses. Analyses for viruses were therefore conducted for three weeks in influent, after conventional treatment, after additional ozonation, and after passing an open dam system at a full-scale treatment plant in Knivsta, Sweden. Viruses were concentrated by adsorption to a positively charged filter, from which they were eluted and pelleted by ultracentrifugation, with a recovery of about 10%. Ion Torrent sequencing was used to analyze influent, leading to the identification of at least 327 viral species, most of which belonged to 25 families with some having unclear classification. Real-time PCR was used to test for 21 human-related viruses in inlet, conventionally treated, and ozone-treated sewage and outlet waters. The viruses identified in influent and further analyzed were adenovirus, norovirus, sapovirus, parechovirus, hepatitis E virus, astrovirus, pecovirus, picobirnavirus, parvovirus, and gokushovirus. Conventional treatment reduced viral concentrations by one to four log10, with the exception of adenovirus and parvovirus, for which the removal was less efficient. Ozone treatment led to a further reduction by one to two log10, but less for adenovirus. This study showed that the amount of all viruses was reduced by conventional sewage treatment. Further ozonation reduced the amounts of several viruses to undetectable levels, indicating that this is a promising technique for reducing the transmission of many pathogenic human viruses.

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Section: Discussionsupporting

confidence: 91%

Differential removal of human pathogenic viruses from sewage by conventional and ozone treatments

Wang

Sikora

Rutgersson

et al. 2018

International Journal of Hygiene and Environmental Health

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“…Those studies that investigated RNA viruses found both bacterial and eukaryotic viruses, with a high abundance of plant viruses of the family Virgaviridae, which includes the tobamovirus pepper mild mottle virus (11, 19). The families of viruses with potential human hosts found in previous metagenomics studies of sewage include Astroviridae, Caliciviridae, Picobirnaviridae and Picornaviridae (13, 19–21), of which only picobirnaviruses were recovered in all wastewater viromes in this study. In contrast, members of the family Reoviridae, represented by the genus Rotavirus, were found in three out of our four wastewater samples, but were not detected in many of the previous studies (19–21).…”

Section: Resultsmentioning

confidence: 58%

Viromic analysis of wastewater input to a river catchment reveals a diverse assemblage of RNA viruses

Adriaenssens

Farkas

Harrison

et al. 2018

Preprint

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13Detection of viruses in the environment is heavily dependent on PCR-based 14 approaches that require reference sequences for primer design. While this strategy 15 can accurately detect known viruses, it will not find novel genotypes, nor emerging 16 and invasive viral species. In this study, we investigated the use of viromics, i.e. 17 high-throughput sequencing of the biosphere viral fraction, to detect human/animal 18 pathogenic RNA viruses in the Conwy river catchment area in Wales, UK. Using a 19 combination of filtering and nuclease treatment, we extracted the viral fraction from 20 wastewater, estuarine river water and sediment, followed by RNASeq analysis on 21 the Illumina HiSeq platform for the discovery of RNA virus genomes. We found a 22 the range of potentially pathogenic viruses that are present in the environment and 37 identify prevalent genotypes. The ultimate goal is to trace the fate of these 38 pathogenic viruses from origin to the point where they are a threat to human health, 39 informing reference-based detection methods and water quality management. 40Recent reviews have proposed the use of viral metagenomics or viromic approaches 58 as an alternative method to test for the presence of pathogenic viruses in the 59 environment (2, 9, 10). Provided the entire viral community is sampled and 60 4 sequenced, novel genotypes or even entirely novel viruses can be detected. 61Potential new viral markers for faecal contamination have already been revealed, 62 such as pepper mild mottle virus and crAssphage (11, 12), among the huge diversity 63 of human viruses found in sludge samples (13). 64In this pilot study, we have used viromics to investigate the presence of human 65 pathogenic RNA viruses in wastewater, estuarine surface water and sediment in a 66 single catchment. The water and sediment samples were collected at, and 67 downstream of, the wastewater treatment plant (Lanrwst, Wales, UK), at the estuary 68 of the river Conwy (Wales, UK) near Morfa beach (Figure 1). To our knowledge, this 69 is the first study to use unamplified environmental viral RNA for sequencing library 70 construction, sequence dataset production and subsequent analysis. Because we 71 used a directional library sequencing protocol on RNA, rather than amplifying to 72 cDNA, we were able to distinguish single-stranded from double-stranded RNA 73 genome fragments. 74

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“…Next generation sequencing is another promising technology, providing a wealth of information on the complex microbial communities in samples, including identification of the diverse range of pathogens and resistance genes present. In particular, analysis of the viruses and resistance genes present via metagenomics has been highlighted as providing potentially key information on novel pathogens as well as re-emerging infectious diseases and AMR (Aarestrup and Woolhouse, 2020;Fernandez-Cassi et al, 2018). Whilst standardisation of protocols of metagenomics remain a challenge, the continued advancements in the technology combined with decreasing costs sequencing have the potential to revolutionise both pathogen and resistance surveillance in wastewater.…”

Section: Markers Of Pathogenic Organismsmentioning

confidence: 99%

Future perspectives of wastewater-based epidemiology: Monitoring infectious disease spread and resistance to the community level

Sims

Kasprzyk-Hordern

2020

Environment International

491

348

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Infectious diseases are acknowledged as one of the most critical threats to global public health today. Climate change, unprecedented population growth with accelerated rates of antimicrobial resistance, have resulted in both the emergence of novel pathogenic organisms and the re-emergence of infections that were once controlled. The consequences have led to an increased vulnerability to infectious diseases globally. The ability to rapidly monitor the spread of diseases is key for prevention, intervention and control, however several limitations exist for current surveillance systems and the capacity to cope with the rapid population growth and environmental changes. Wastewater-Based Epidemiology (WBE) is a new epidemiology tool that has potential to act as a complementary approach for current infectious disease surveillance systems and an early warning system for disease outbreaks. WBE postulates that through the analysis of population pooled wastewater, infectious disease and resistance spread, the emergence of new disease outbreak to the community level can be monitored comprehensively and in real-time. This manuscript provides critical overview of current infectious disease surveillance status, as well as it introduces WBE and its recent advancements. It also provides recommendations for further development required for WBE application as an effective tool for infectious disease surveillance.

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Metagenomics for the study of viruses in urban sewage as a tool for public health surveillance

Cited by 142 publications

References 87 publications

Differential removal of human pathogenic viruses from sewage by conventional and ozone treatments

Differential removal of human pathogenic viruses from sewage by conventional and ozone treatments

Viromic analysis of wastewater input to a river catchment reveals a diverse assemblage of RNA viruses

Future perspectives of wastewater-based epidemiology: Monitoring infectious disease spread and resistance to the community level

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