Surveillance for SARS-CoV-2 and its variants in wastewater of tertiary care hospitals correlates with increasing case burden and outbreaks

Nicole Acosta, Maria A. Bautista, Barbara J. Waddell, Kristine Du, Janine McCalder, Puja Pradhan, Navid Sedaghat, Chloe Papparis, Alexander Buchner Beaudet, Jianwei Chen, Jennifer Van Doorn, Kevin Xiang, Leslie Chan, Laura Vivas, Kashtin Low, Xuewen Lu, Jangwoo Lee, Paul Westlund, Thierry Chekouo, Xiaotian DaiJason Cabaj, Srijak Bhatnagar, Norma Ruecker, Gopal Achari, Rhonda G. Clark, Craig Pearce, Joe J. Harrison, Jon Meddings, Jenine Leal, Jennifer Ellison, Bayan Missaghi, Jamil N. Kanji, Oscar Larios, Elissa Rennert-May, Joseph Kim, Steve E. Hrudey, Bonita E. Lee, Xiaoli Pang, Kevin Frankowski, John Conly, Casey R.J. Hubert, Michael D. Parkins

Research output: Contribution to journalJournal Articlepeer-review

10 Citations (Scopus)

Abstract

Wastewater-based SARS-CoV-2 surveillance enables unbiased and comprehensive monitoring of defined sewersheds. We performed real-time monitoring of hospital wastewater that differentiated Delta and Omicron variants within total SARS-CoV-2-RNA, enabling correlation to COVID-19 cases from three tertiary-care facilities with >2100 inpatient beds in Calgary, Canada. RNA was extracted from hospital wastewater between August/2021 and January/2022, and SARS-CoV-2 quantified using RT-qPCR. Assays targeting R203M and R203K/G204R established the proportional abundance of Delta and Omicron, respectively. Total and variant-specific SARS-CoV-2 in wastewater was compared to data for variant specific COVID-19 hospitalizations, hospital-acquired infections, and outbreaks. Ninety-six percent (188/196) of wastewater samples were SARS-CoV-2 positive. Total SARS-CoV-2 RNA levels in wastewater increased in tandem with total prevalent cases (Delta plus Omicron). Variant-specific assessments showed this increase to be mainly driven by Omicron. Hospital-acquired cases of COVID-19 were associated with large spikes in wastewater SARS-CoV-2 and levels were significantly increased during outbreaks relative to nonoutbreak periods for total SARS-CoV2, Delta and Omicron. SARS-CoV-2 in hospital wastewater was significantly higher during the Omicron-wave irrespective of outbreaks. Wastewater-based monitoring of SARS-CoV-2 and its variants represents a novel tool for passive COVID-19 infection surveillance, case identification, containment, and potentially to mitigate viral spread in hospitals.

Original languageEnglish
Article numbere28442
JournalJournal of Medical Virology
Volume95
Issue number2
DOIs
Publication statusPublished - Feb. 2023

Keywords

  • COVID-19
  • RT-qPCR
  • hospital-acquired infection
  • prevalent
  • variant of concern
  • wastewater-based surveillance

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