Detection of Enterovirus D68 in Wastewater Samples from the UK between July and November 2021
Abstract
:1. Introduction
2. Materials and Methods
2.1. Wastewater Sample Collection and Processing
2.2. Modified Pan-EV Entire-Capsid Coding Region RT-PCR Amplification (mECRA)
- Primers 5′NCR (5′-TGGCGGAACCGACTACTTTGGGTG-3′) and CRE-R (5′-TCAATACGGTGTTTGCTCTTGAACTG-3′);
- Primers MM_EV_F2 (5′-CAGCGGAACCGACTACTTT-3′) and MM_EV_R1 (5′-AATACGGCATTTGGACTTGAACTGT-3′).
2.3. VP1-Nested PCR Amplification and Nucleotide Sequence Analysis of the VP1 Coding Region of EV-D68 Strains by Sanger Sequencing
- Universal primers: D68_VP1_PubF (5′-ACCATTTACATGCRGCAGAGG-3′) and D68-2ARpub (5′-ACATCTGAYTGCCARTCYAC-3′);
- Clade B3 primers: D68_VP1_PubF (5′-ACCATTTACATGCRGCAGAGG-3′) and 2016_D68_VP1R (5′-CCTGGACCAGTAGTCACTATATTATG-3′);
- Clade D primers: 14.001-D68-VP1F (5′-ATTGGACAACTAGAGCATTTACATGAG-3′) and 14.001-D68-VP1R (5′-CAGTATTCACTAACCGAATGTCGTG-3′).
2.4. NGS Analysis of mECRA Products
2.5. Phylogenetic Analysis of EV-D68 Strains from Wastewater Samples
3. Results
3.1. Detection of EV-D68 in Wastewater Samples by VP1-Nested PCR and Nucleotide Sequence Analysis
VP1-Nested PCR Positive for Enterovirus D68 (%) 1 | ||||
---|---|---|---|---|
Location | Date of Collection | Universal Primers | Clade B3 Primers | Clade D Primers |
London | 13 July 2021 | 0 | 16.7 | 0 |
Glasgow | 29 July 2021 | 16.7 | 83.3 | 0 |
London | 10 August 2021 | 33.3 | 50 | 0 |
Glasgow | 26 August 2021 | 83.3 | 33.3 | 0 |
London | 14 September 2021 | 50 | 50 | 0 |
London | 28 September 2021 | 83.3 | 100 | 33.3 |
Glasgow | 29 September 2021 | 66.7 | 100 | 0 |
London | 12 October 2021 | 100 | 100 | 50 |
London | 26 October 2021 | 83.3 | 100 | 50 |
Glasgow | 27 October 2021 | 66.7 | 100 | 83.3 |
London | 23 November 2021 | 100 | 100 | 0 |
Glasgow | 24 November 2021 | 100 | 100 | 33.3 |
3.2. NGS Analysis of EV-D68 VP1 Sequences from Wastewater Samples
3.3. Phylogenetic Analysis of EV-D68 Strains Identified in UK Wastewater Samples
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
EV | Enterovirus |
E- | Echovirus |
CV- | Coxsackievirus |
NGS | Next-Generation Sequencing |
ES | Environmental Surveillance |
ORF | Open Reading Frame |
Country Abbreviations | USA, United States; NET, Netherland; IND, India; JPN, Japan; CHN, China; THA, Thailand; GER, Germany; MAL, Malaysia; DNK, Denmark; TAI, Taiwan; FRA, France; HKN, Hong Kong; SAF, South Africa; SEN, Senegal; SWE, Sweden; ITA, Italy; MEX, Mexico; PHI, Philippines; SPA, Spain; CAN, Canada; KEN, Kenya; SCO, Scotland; ENG, England; HAI, Haiti; TZN, Tanzania; NZL, New Zealand. |
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Tedcastle, A.; Wilton, T.; Pegg, E.; Klapsa, D.; Bujaki, E.; Mate, R.; Fritzsche, M.; Majumdar, M.; Martin, J. Detection of Enterovirus D68 in Wastewater Samples from the UK between July and November 2021. Viruses 2022, 14, 143. https://doi.org/10.3390/v14010143
Tedcastle A, Wilton T, Pegg E, Klapsa D, Bujaki E, Mate R, Fritzsche M, Majumdar M, Martin J. Detection of Enterovirus D68 in Wastewater Samples from the UK between July and November 2021. Viruses. 2022; 14(1):143. https://doi.org/10.3390/v14010143
Chicago/Turabian StyleTedcastle, Alison, Thomas Wilton, Elaine Pegg, Dimitra Klapsa, Erika Bujaki, Ryan Mate, Martin Fritzsche, Manasi Majumdar, and Javier Martin. 2022. "Detection of Enterovirus D68 in Wastewater Samples from the UK between July and November 2021" Viruses 14, no. 1: 143. https://doi.org/10.3390/v14010143