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SARS-CoV-2 variant trends in Ireland: Wastewater-based epidemiology and clinical surveillance.
Reynolds, Liam J; Gonzalez, Gabriel; Sala-Comorera, Laura; Martin, Niamh A; Byrne, Alannah; Fennema, Sanne; Holohan, Niamh; Kuntamukkula, Sailusha Ratnam; Sarwar, Natasha; Nolan, Tristan M; Stephens, Jayne H; Whitty, Megan; Bennett, Charlene; Luu, Quynh; Morley, Ursula; Yandle, Zoe; Dean, Jonathan; Joyce, Eadaoin; O'Sullivan, John J; Cuddihy, John M; McIntyre, Angeline M; Robinson, Eve P; Dahly, Darren; Fletcher, Nicola F; Carr, Michael; De Gascun, Cillian; Meijer, Wim G.
  • Reynolds LJ; UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland.
  • Gonzalez G; National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin, Ireland; International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, N20 W10 Kita-ku, Sapporo 001-0020, Japan.
  • Sala-Comorera L; UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland.
  • Martin NA; UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland.
  • Byrne A; UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland.
  • Fennema S; UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland.
  • Holohan N; UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland.
  • Kuntamukkula SR; UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland.
  • Sarwar N; UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland.
  • Nolan TM; UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland.
  • Stephens JH; UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland.
  • Whitty M; UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland.
  • Bennett C; National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin, Ireland.
  • Luu Q; National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin, Ireland.
  • Morley U; National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin, Ireland.
  • Yandle Z; National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin, Ireland.
  • Dean J; National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin, Ireland.
  • Joyce E; Irish Water, Colvill House, 24-26 Talbot Street, Dublin 1, Ireland.
  • O'Sullivan JJ; UCD School of Civil Engineering, UCD Dooge Centre for Water Resources Research and UCD Earth Institute, University College Dublin, Dublin 4, Ireland.
  • Cuddihy JM; HSE - Health Protection Surveillance Centre, Dublin, Ireland.
  • McIntyre AM; HSE - Health Protection Surveillance Centre, Dublin, Ireland.
  • Robinson EP; HSE - Health Protection Surveillance Centre, Dublin, Ireland.
  • Dahly D; Health Research Board Clinical Research Facility, University College Cork, Cork, Ireland.
  • Fletcher NF; UCD School of Veterinary Medicine and UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland.
  • Carr M; National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin, Ireland; International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, N20 W10 Kita-ku, Sapporo 001-0020, Japan.
  • De Gascun C; National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin, Ireland.
  • Meijer WG; UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland. Electronic address: wim.meijer@ucd.ie.
Sci Total Environ ; 838(Pt 2): 155828, 2022 Sep 10.
Article in English | MEDLINE | ID: covidwho-1852047
ABSTRACT
SARS-CoV-2 RNA quantification in wastewater is an important tool for monitoring the prevalence of COVID-19 disease on a community scale which complements case-based surveillance systems. As novel variants of concern (VOCs) emerge there is also a need to identify the primary circulating variants in a community, accomplished to date by sequencing clinical samples. Quantifying variants in wastewater offers a cost-effective means to augment these sequencing efforts. In this study, SARS-CoV-2 N1 RNA concentrations and daily loadings were determined and compared to case-based data collected as part of a national surveillance programme to determine the validity of wastewater surveillance to monitor infection spread in the greater Dublin area. Further, sequencing of clinical samples was conducted to determine the primary SARS-CoV-2 lineages circulating in Dublin. Finally, digital PCR was employed to determine whether SARS-CoV-2 VOCs, Alpha and Delta, were quantifiable from wastewater. No lead or lag time was observed between SARS-CoV-2 wastewater and case-based data and SARS-CoV-2 trends in Dublin wastewater significantly correlated with the notification of confirmed cases through case-based surveillance preceding collection with a 5-day average. This demonstrates that viral RNA in Dublin's wastewater mirrors the spread of infection in the community. Clinical sequence data demonstrated that increased COVID-19 cases during Ireland's third wave coincided with the introduction of the Alpha variant, while the fourth wave coincided with increased prevalence of the Delta variant. Interestingly, the Alpha variant was detected in Dublin wastewater prior to the first genome being sequenced from clinical samples, while the Delta variant was identified at the same time in clinical and wastewater samples. This work demonstrates the validity of wastewater surveillance for monitoring SARS-CoV-2 infections and also highlights its effectiveness in identifying circulating variants which may prove useful when sequencing capacity is limited.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study Topics: Variants Limits: Humans Country/Region as subject: Europa Language: English Journal: Sci Total Environ Year: 2022 Document Type: Article Affiliation country: J.scitotenv.2022.155828

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study Topics: Variants Limits: Humans Country/Region as subject: Europa Language: English Journal: Sci Total Environ Year: 2022 Document Type: Article Affiliation country: J.scitotenv.2022.155828