Comparison of metagenomic and targeted methods for sequencing human pathogenic viruses from wastewater

mBio, Journal Year: 2023, Volume and Issue: 14(6)

Published: Oct. 25, 2023

Most public health initiatives that monitor viruses in wastewater have utilized quantitative polymerase chain reaction (PCR) and whole genome PCR sequencing, mirroring techniques used for viral epidemiology individuals. These require prior knowledge of the target are limited to monitoring individual or small groups viruses. Metagenomic sequencing may offer an alternative strategy a broad spectrum wastewater, including novel emerging pathogens. In this study, while amplicon gave high coverage, untargeted shotgun total nucleic acid samples was unable detect human pathogenic with enough sensitivity use genomic epidemiology. Enrichment libraries respiratory using hybrid-capture technology provided genotypic information on range simultaneously, indicating strong potential surveillance. This type targeted metagenomics could be diverse targets, such as pathogens antimicrobial resistance genes, environmental samples.

Language: Английский

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Evaluation of the Impact of Concentration and Extraction Methods on the Targeted Sequencing of Human Viruses from Wastewater

Environmental Science & Technology, Journal Year: 2024, Volume and Issue: 58(19), P. 8239 - 8250

Published: May 1, 2024

Sequencing human viruses in wastewater is challenging due to their low abundance compared the total microbial background. This study impact of four virus concentration/extraction methods (Innovaprep, Nanotrap, Promega, and Solids extraction) on probe-capture enrichment for followed by sequencing. Different yielded distinct profiles. Innovaprep ultrafiltration (following solids removal) had highest sequencing sensitivity richness, resulting successful assembly several near-complete genomes. However, it was less sensitive detecting SARS-CoV-2 digital polymerase chain reaction (dPCR) Promega Nanotrap. Across all preparation methods, astroviruses polyomaviruses were most highly abundant viruses, rare. These findings suggest that success can be increased using reduce nontarget nucleic acids extract, though absolute concentration extracted acid, as indicated Qubit, targeted dPCR, may not directly related performance. Further, broadly panels capture viral diversity but risks losing signals specific low-abundance viruses. Overall, this highlights importance aligning wet lab bioinformatic with goals when employing from wastewater.

Language: Английский

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A retrospective longitudinal study of adenovirus group F, norovirus GI and GII, rotavirus, and enterovirus nucleic acids in wastewater solids at two wastewater treatment plants: solid-liquid partitioning and relation to clinical testing data

mSphere, Journal Year: 2024, Volume and Issue: 9(3)

Published: Feb. 27, 2024

Enteric infections are important causes of morbidity and mortality, yet clinical surveillance is limited. Wastewater-based epidemiology (WBE) has been used to study community circulation individual enteric viruses panels respiratory diseases, but there limited work studying the concurrent a suite viruses. A retrospective WBE was carried out at two wastewater treatment plants located in California, United States. Using digital droplet polymerase chain reaction (PCR), we measured concentrations human adenovirus group F, enteroviruses, norovirus genogroups I II, rotavirus nucleic acids solids times per week for 26 months (

Language: Английский

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Adeno-Associated Virus 2 and Human Adenovirus F41 in Wastewater during Outbreak of Severe Acute Hepatitis in Children, Ireland

Emerging infectious diseases, Journal Year: 2023, Volume and Issue: 29(4), P. 751 - 760

Published: March 26, 2023

During April-July 2022, outbreaks of severe acute hepatitis unknown etiology (SAHUE) were reported in 35 countries. Five percent cases required liver transplantation, and 22 patients died. Viral metagenomic studies clinical samples from SAHUE showed a correlation with human adenovirus F type 41 (HAdV-F41) adeno-associated virus 2 (AAV2). To explore the association between those DNA viruses children Ireland, we quantified HAdV-F41 AAV2 collected wastewater treatment plant serving 40% Ireland's population. We noted high circulation community cases. Next-generation sequencing hexon demonstrated was predominant HAdV circulating. Our environmental analysis increased prevalence during outbreak. findings highlight how sampling could aid surveillance for respiratory species.

Language: Английский

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Pathogenicity and virulence of human adenovirus F41: Possible links to severe hepatitis in children

Virulence, Journal Year: 2023, Volume and Issue: 14(1)

Published: Aug. 6, 2023

Over 100 human adenoviruses (HAdVs) have been isolated and allocated to seven species, A-G. Species F comprises two members-HAdV-F40 HAdV-F41. As their primary site of infection is the gastrointestinal tract they termed, with species A, enteric adenoviruses. HAdV-F40 HAdV-F41 are a common cause gastroenteritis diarrhoea in children. Partly because difficulties propagating viruses laboratory, due restrictions on growth many cell lines, our knowledge properties individual viral proteins limited. However, structure has recently determined by cryo-electron microscopy. The overall similar those HAdV-C5 HAdV-D26 although some differences. sequence arrangement hexon hypervariable region 1 (HVR1) C-terminal protein IX differ. Variations penton base HVR1 may play role facilitating intestinal cells A unique feature F41, among adenoviruses, presence expression fibre genes, giving long short proteins. This also contribute tropism these viruses. linked recent outbreak severe acute hepatitis "of unknown origin" young Further investigation shown very high prevalence adeno-associated virus-2 liver and/or plasma cohorts patients. These observations proved controversial as had not reported infect AAV-2 generally considered harmless.

Language: Английский

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Assessment of Gastroenteric Viruses in Marketed Bivalve Mollusks in the Tourist Cities of Rio de Janeiro, Brazil, 2022

Viruses, Journal Year: 2024, Volume and Issue: 16(3), P. 317 - 317

Published: Feb. 20, 2024

This study investigated the prevalence and genetic diversity of gastroenteric viruses in mussels oysters Rio de Janeiro, Brazil. One hundred thirty-four marketed bivalve samples were obtained between January December 2022. The viral analysis was performed according to ISO/TS 15216, screening revealed detection norovirus GII/GI (40.3%), sapovirus (SaV; 12.7%), human mastadenovirus (7.5%), rotavirus A (RVA; 5.9%). In total, 44.8% (60) shellfish tested positive for one or more viruses, 46.7% (28/60) a single agent, 26.7% (16) two agents, 8.3% (5) three 13.3% (8) four agents. Additionally, mussel contaminated with five (5%, 3/60). Norovirus GII showed highest mean load (3.4 × 105 GC/g), followed by SaV (1.4 104 RVA (1.1 (3.9 103 GI (6.7 102 GC/g). Molecular characterization that recovered strains belonged genotypes GII.2, GII.6, GII.9, GII.17, GII.27; GI.1 GIV.1; G6, G8, P[8]-III, types F40 F41. GII.27 characterized this is only strain genotype reported highlights dissemination present commercialized bivalves touristic area, indicating potential risk health contribution propagation emerging pathogens.

Language: Английский

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Genomic Analysis and Surveillance of Respiratory Syncytial Virus Using Wastewater-Based Epidemiology

The Journal of Infectious Diseases, Journal Year: 2024, Volume and Issue: 230(4), P. e895 - e904

Published: April 18, 2024

Respiratory syncytial virus (RSV) causes severe infections in infants, immunocompromised or elderly individuals resulting annual epidemics of respiratory disease. Currently, limited clinical surveillance and the lack predictable seasonal dynamics limit public health response. Wastewater-based epidemiology (WBE) has recently been used globally as a key metric determining prevalence acute syndrome coronavirus 2 community, but its application to other viruses is limited. In this study, we present an integrated genomic WBE approach, applying reverse-transcription quantitative polymerase chain reaction partial G-gene sequencing track RSV levels variants community. We report increasing detection wastewater concomitant with numbers positive cases. Analysis wastewater-derived sequences permitted identification distinct circulating lineages within between seasons. Altogether, our platform potential complement ongoing global aid management by informing timely deployment pharmaceutical nonpharmaceutical interventions.

Language: Английский

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Genomic Analysis and Surveillance of Respiratory Syncytial Virus (RSV) Using Wastewater-Based Epidemiology (WBE)

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: July 24, 2023

Abstract Respiratory syncytial virus (RSV) causes severe infections in infants, immunocompromised or elderly individuals resulting annual epidemics of respiratory disease. Currently, limited clinical RSV surveillance and the lack predictable seasonal dynamics limits public health response. Wastewater-based epidemiology (WBE) has capacity to determine levels health-associated biomarkers recently been used globally as a key metric determining prevalence SARS-CoV-2 community. However, application genomic WBE for other viruses is limited. In this study, we present an integrated approach, using RT-qPCR partial sequencing G gene monitor variants community across 2 years encompassing two periods high positivity Northern Ireland. We report increasing detection wastewater concomitant with numbers positive cases. Furthermore, analysis wastewater-derived sequences permitted subtyping, genotyping, identification distinct circulating lineages within between seasons. Altogether, our platform potential complement ongoing global efforts aid management by informing timely deployment pharmaceutical non-pharmaceutical interventions.

Language: Английский

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Use of Capsid Integrity-qPCR for Detecting Viral Capsid Integrity in Wastewater

Viruses, Journal Year: 2023, Volume and Issue: 16(1), P. 40 - 40

Published: Dec. 26, 2023

Quantifying viruses in wastewater via RT-qPCR provides total genomic data but does not indicate the virus capsid integrity or potential risk for human infection. Assessing sewage is important wastewater-based surveillance, since discharged effluent may pose a public health hazard. While assays using cell cultures can provide this information, they require specialised laboratories and expertise. One solution to overcome limitation use of photo-reactive monoazide dyes (e.g., propidium [PMAxx]) integrity-RT-qPCR assay (ci-RT-qPCR). In study, we tested efficiency PMAxx dye at 50 μM 100 concentrations on live heat-inactivated model commonly detected wastewater, including adenovirus (AdV), hepatitis A (HAV), influenza (IAV), norovirus GI (NoV GI). The concentration effectively differentiated from all targets buffer solution. This method was then applied samples (n = 19) detection encapsulated AdV, enterovirus (EV), HAV, IAV, B (IBV), NoV GI, GII, SARS-CoV-2. Samples were negative IBV positive EV, PMAxx-treated samples, GII showed −0.52–1.15, 0.9–1.51, 0.31–1.69 log reductions integrity, indicating high degree potentially infectious wastewater. contrast, SARS-CoV-2 only after treatment, absence virus. conclusion, study demonstrates utility evaluate across diverse range monitored

Language: Английский

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Wastewater monitoring of human and avian influenza A viruses in Northern Ireland: a genomic surveillance study

The Lancet Microbe, Journal Year: 2024, Volume and Issue: unknown, P. 100933 - 100933

Published: Oct. 1, 2024

Influenza A viruses (IAVs) are significant pathogens of humans and other animals. Although endemic in birds, novel IAV strains can emerge, jump species, cause epidemics, like the latest variant H5N1. Wastewater-based epidemiology (WBE) has been shown capable detecting human IAVs. We aimed to assess whether whole-genome sequencing (WGS) IAVs from wastewater is possible be used discriminate between circulating any non-human IAVs, such as those avian origin.

Language: Английский

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