Metabarcoding of Hepatitis E Virus Genotype 3 and Norovirus GII from Wastewater Samples in England Using Nanopore Sequencing.
Environmental transmission
Hepatitis E virus
Metabarcoding
Nanopore sequencing
Norovirus
Wastewater-based epidemiology
Journal
Food and environmental virology
ISSN: 1867-0342
Titre abrégé: Food Environ Virol
Pays: United States
ID NLM: 101483831
Informations de publication
Date de publication:
Dec 2023
Dec 2023
Historique:
received:
20
05
2023
accepted:
29
09
2023
medline:
17
11
2023
pubmed:
1
11
2023
entrez:
1
11
2023
Statut:
ppublish
Résumé
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 three 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.
Identifiants
pubmed: 37910379
doi: 10.1007/s12560-023-09569-w
pii: 10.1007/s12560-023-09569-w
pmc: PMC7615314
mid: EMS190417
doi:
Substances chimiques
Wastewater
0
RNA, Viral
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
292-306Subventions
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 109356
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 109356/Z/15/Z
Pays : United Kingdom
Informations de copyright
© 2023. Crown.
Références
Clin Microbiol Rev. 2015 Jan;28(1):134-64
pubmed: 25567225
J Clin Med. 2020 Jan 24;9(2):
pubmed: 31991629
BMC Infect Dis. 2004 Sep 21;4:37
pubmed: 15383150
Water Res. 2021 Oct 15;205:117710
pubmed: 34607084
Clin Nephrol. 2018 Dec;90(6):427-430
pubmed: 30232953
J Infect Dis. 2019 Jul 31;220(5):802-810
pubmed: 31107958
J Appl Microbiol. 2019 Jan;126(1):324-331
pubmed: 30315674
J Virol Methods. 2002 Feb;100(1-2):107-14
pubmed: 11742657
Emerg Infect Dis. 2021 Apr;27(6):1654-1661
pubmed: 34013866
J Clin Microbiol. 2003 Apr;41(4):1548-57
pubmed: 12682144
Sci Rep. 2021 Mar 8;11(1):5372
pubmed: 33686189
Euro Surveill. 2022 Jun;27(23):
pubmed: 35686567
Nucleic Acids Res. 2016 Jul 8;44(W1):W242-5
pubmed: 27095192
Viruses. 2019 Jul 05;11(7):
pubmed: 31284466
Viruses. 2020 Oct 09;12(10):
pubmed: 33050264
Clin Lab. 2016;62(4):689-96
pubmed: 27215089
Food Environ Virol. 2019 Jun;11(2):138-148
pubmed: 30900141
J Clin Virol. 2011 Jun;51(2):121-5
pubmed: 21514213
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Emerg Infect Dis. 2011 Mar;17(3):412-8
pubmed: 21392431
J Virol Methods. 2012 Dec;186(1-2):157-60
pubmed: 22871672
Emerg Infect Dis. 2021 May;27(5):1438-1445
pubmed: 33900173
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W43-6
pubmed: 17452344
Nucleic Acids Res. 2022 Jul 5;50(W1):W276-W279
pubmed: 35412617
Bioinformatics. 2012 Apr 15;28(8):1166-7
pubmed: 22368248
Appl Environ Microbiol. 2009 Dec;75(23):7350-5
pubmed: 19820160
J Gen Virol. 2020 Jul;101(7):692-698
pubmed: 32469300
Euro Surveill. 2016 Jun 29;22(26):
pubmed: 28681720
Gigascience. 2021 Feb 16;10(2):
pubmed: 33590861
PLoS One. 2015 Apr 23;10(4):e0122102
pubmed: 25906163
Food Environ Virol. 2018 Jun;10(2):217-221
pubmed: 29442296
J Viral Hepat. 2021 Jan;28(1):196-204
pubmed: 32869414
Environ Sci Technol Lett. 2020 May 20;7(7):511-516
pubmed: 37566285
Appl Environ Microbiol. 1994 Aug;60(8):2963-70
pubmed: 8085832
Genome Res. 2017 May;27(5):722-736
pubmed: 28298431
J Infect Dis. 2014 Apr 15;209(8):1212-8
pubmed: 24273173
Viruses. 2021 Jun 17;13(6):
pubmed: 34204376
Mol Biol Evol. 2015 Jan;32(1):268-74
pubmed: 25371430
Appl Environ Microbiol. 2012 Aug;78(16):5812-7
pubmed: 22685151
PLoS One. 2017 Apr 27;12(4):e0176414
pubmed: 28448527
Clin Infect Dis. 2016 Feb 1;62(3):351-7
pubmed: 26429341
J Virol Methods. 2006 Jan;131(1):65-71
pubmed: 16125257
J Virol Methods. 2005 Jan;123(1):1-7
pubmed: 15582692
Viruses. 2019 May 17;11(5):
pubmed: 31108942
Food Microbiol. 2018 Dec;76:390-395
pubmed: 30166165
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Emerg Infect Dis. 2015 Aug;21(8):1396-401
pubmed: 26196216
Emerg Infect Dis. 2018 May;24(5):920-923
pubmed: 29664371
Proc Natl Acad Sci U S A. 2018 Nov 6;115(45):11495-11500
pubmed: 30348781
Transbound Emerg Dis. 2018 Feb;65(1):e25-e31
pubmed: 28497542
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
PLoS Pathog. 2017 Jan 19;13(1):e1006136
pubmed: 28103318
J Infect Dis. 2016 Aug 15;214(4):556-64
pubmed: 27354370