Early Warning Measurement of SARS-CoV-2 Variants of Concern in Wastewaters by Mass Spectrometry

Jiaxi Peng; Jianxian Sun; Minqing Ivy Yang; Richard M Gibson; Eric J Arts; Abayomi S Olabode; Art F Y Poon; Xianyao Wang; Aaron R Wheeler; Elizabeth A Edwards; Hui Peng

doi:10.1021/acs.estlett.2c00280

Early Warning Measurement of SARS-CoV-2 Variants of Concern in Wastewaters by Mass Spectrometry

Environ Sci Technol Lett. 2022 Jun 17;9(7):638-644. doi: 10.1021/acs.estlett.2c00280. eCollection 2022 Jul 12.

Authors

Jiaxi Peng^{1

2

3}, Jianxian Sun¹, Minqing Ivy Yang⁴, Richard M Gibson⁵, Eric J Arts⁵, Abayomi S Olabode⁵, Art F Y Poon⁵, Xianyao Wang¹, Aaron R Wheeler^{1

2

3}, Elizabeth A Edwards⁴, Hui Peng^{1

6}

Affiliations

¹ Department of Chemistry, University of Toronto, 80 St George Street, Toronto, Ontario M5S 3H6, Canada.
² Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.
³ Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada.
⁴ Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada.
⁵ Department of Microbiology and Immunology, Western University, 1151 Richmond Street, London, Ontario N6A 5C1, Canada.
⁶ School of the Environment, University of Toronto, 80 St George Street, Toronto, Ontario M5S 3H6, Canada.

PMID: 37552744
DOI: 10.1021/acs.estlett.2c00280

Abstract

Wastewater surveillance has rapidly emerged as an early warning tool to track COVID-19. However, the early warning measurement of new SARS-CoV-2 variants of concern (VOCs) in wastewaters remains a major challenge. We herein report a rapid analytical strategy for quantitative measurement of VOCs, which couples nested polymerase chain reaction and liquid chromatography-mass spectrometry (nPCR-LC-MS). This method showed a greater selectivity than the current allele-specific quantitative PCR (AS-qPCR) for tracking new VOC and allowed the detection of multiple signature mutations in a single measurement. By measuring the Omicron variant in wastewaters across nine Ontario wastewater treatment plants serving over a three million population, the nPCR-LC-MS method demonstrated a better quantification accuracy than next-generation sequencing (NGS), particularly at the early stage of community spreading of Omicron. This work addresses a major challenge for current SARS-CoV-2 wastewater surveillance by rapidly and accurately measuring VOCs in wastewaters for early warning.