Metabarcoding of Hepatitis E virus genotype 3 and Norovirus GII from wastewater samples in England using nanopore sequencing
dc.contributor.author | Treagus, S | |
dc.contributor.author | Lowther, J | |
dc.contributor.author | Longdon, B | |
dc.contributor.author | Gaze, W | |
dc.contributor.author | Baker-Austin, C | |
dc.contributor.author | Ryder, D | |
dc.contributor.author | Batista, FM | |
dc.date.accessioned | 2023-10-05T10:18:03Z | |
dc.date.issued | 2023-11-01 | |
dc.date.updated | 2023-10-05T09:21:20Z | |
dc.description.abstract | Norovirus is one of the largest causes of gastroenteritis worldwide, and Hepatitis E virus (HEV) is an emerging pathogen that has become the most dominant cause of acute viral hepatitis in recent years. The presence of norovirus and HEV has been reported within wastewater in many countries previously. Here we used amplicon deep sequencing (metabarcoding) to identify norovirus and HEV strains in wastewater samples from England collected in 2019 and 2020. For HEV, we sequenced a fragment of the RNA-dependent RNA polymerase (RdRp) gene targeting genotype 3 strains. For norovirus, we sequenced the 5’ portion of the major capsid protein gene (VP1) of genogroup II strains. Sequencing of the wastewater samples revealed eight different genotypes of norovirus GII (GII.2, GII.3, GII.4, GII.6, GII.7, GII.9, GII.13 and GII.17). Genotypes GII.3 and GII.4 were the most commonly found. The HEV metabarcoding assay was able to identify HEV genotype 3 strains in some samples with a very low viral concentration determined by RT-qPCR. Analysis showed that most HEV strains found in influent wastewater were typed as G3c and G3e and were likely to have originated from humans or swine. However, the small size of the HEV nested PCR amplicon could cause issues with typing, and so this method is more appropriate for samples with high CTs where methods targeting longer genomic regions are unlikely to be successful. This is the first report of HEV RNA in wastewater in England. This study demonstrates the utility of wastewater sequencing and the need for wider surveillance of norovirus and HEV within host species and environments. | en_GB |
dc.description.sponsorship | Cefas internal Seedcorn project | en_GB |
dc.description.sponsorship | Seafood Innovation Fund UK | en_GB |
dc.description.sponsorship | University of Exeter | en_GB |
dc.description.sponsorship | Wellcome Trust | en_GB |
dc.description.sponsorship | Royal Society | en_GB |
dc.identifier.citation | Published 1 November 2023 | en_GB |
dc.identifier.doi | 10.1007/s12560-023-09569-w | |
dc.identifier.grantnumber | DP422 | en_GB |
dc.identifier.grantnumber | RD011 | en_GB |
dc.identifier.grantnumber | 109356/Z/15/Z | en_GB |
dc.identifier.uri | http://hdl.handle.net/10871/134175 | |
dc.identifier | ORCID: 0000-0001-6936-1697 (Longdon, Ben) | |
dc.language.iso | en | en_GB |
dc.publisher | Springer | en_GB |
dc.rights | © Crown 2023. Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ | en_GB |
dc.subject | Hepatitis E virus | en_GB |
dc.subject | Norovirus | en_GB |
dc.subject | nanopore sequencing | en_GB |
dc.subject | metabarcoding | en_GB |
dc.subject | environmental transmission | en_GB |
dc.subject | wastewater-based epidemiology | en_GB |
dc.title | Metabarcoding of Hepatitis E virus genotype 3 and Norovirus GII from wastewater samples in England using nanopore sequencing | en_GB |
dc.type | Article | en_GB |
dc.date.available | 2023-10-05T10:18:03Z | |
dc.identifier.issn | 1867-0342 | |
dc.description | This is the final version. Available on open access from Springer via the DOI in this record | en_GB |
dc.description | Data Availability: See Online Resources for supplementary materials, including bioinformatics scripts. Sequences can be found in GenBank under accession numbers OQ913488 to OQ913500 and OQ918704 to OQ918713. | en_GB |
dc.description | Code Availability: See Online Resources | |
dc.identifier.journal | Food and Environmental Virology | en_GB |
dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | en_GB |
dcterms.dateAccepted | 2023-09-29 | |
dcterms.dateSubmitted | 2023-05-20 | |
rioxxterms.version | VoR | en_GB |
rioxxterms.licenseref.startdate | 2023-09-29 | |
rioxxterms.type | Journal Article/Review | en_GB |
refterms.dateFCD | 2023-10-05T09:21:22Z | |
refterms.versionFCD | AM | |
refterms.dateFOA | 2023-11-10T16:04:17Z | |
refterms.panel | A | en_GB |
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Except where otherwise noted, this item's licence is described as © Crown 2023. Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/