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

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.

Graphene Multiplexed Sensor for Point-of-Need Viral Wastewater-Based Epidemiology

“…We achieved limits of detection (see Table 1) one to two orders of magnitude better than HPLC-MS (Fig. 5) (Dollman, Griffin, and Downard 2020; Nikolaev et al 2020; Peng et al 2022; Lara-Jacobo et al 2022; Kasprzyk-Hordern et al 2023; Mestankova et al 2012) and below the levels needed for effective early interventions (Peng et al 2022). Results are obtained using a 1 cm 2 chip in just over one hour with minimal human intervention and without bulky, expensive lab equipment or costly reagents.…”

“…We achieved limits of detection (see Table 1) one to two orders of magnitude better than HPLC-MS (Fig. 5) (Dollman, Griffin, and Downard 2020;Nikolaev et al 2020;Peng et al 2022;Lara-Jacobo et al 2022;Kasprzyk-Hordern et al 2023;Mestankova et al 2012) and below the levels needed for effective early interventions (Peng et al 2022).…”

“…In the case of LC-MS, LODs between 10 5 – 10 6 copies per nasopharynx sample (Dollman, Griffin, and Downard 2020; Nikolaev et al 2020) have been reported. While LC-MS has been used to detect SARS-CoV-2 in wastewater (Peng et al 2022; Lara-Jacobo et al 2022), no detection limit has yet to be reported. So-called “rapid tests,” on the other hand, while having short analysis time, typically rely on LFIA, which to the best of our knowledge have not shown the ability to rapidly sense the low level of virus in unprocessed wastewater.…”

Advances in virus detection methods for wastewater-based epidemiological applications

“…A recent study has integrated nested PCR and liquid chromatography-mass spectrometry (LC-MS) in the detection of the SARS-CoV-2 Alpha, Delta, Omicron variants in wastewater samples [ 70 ]. The MS method was used to detect the VOCs based on the differences of their molecular weights and also eliminated the need to develop allele-specific primers or probes.…”

Distance-Regulated Photoelectrochemical Sensor “Signal-On” and “Signal-Off” Transitions for the Multiplexed Detection of Viruses Exposed in the Aquatic Environment

“…As nucleic acid detection remains the “gold standard” for virus detection, the development of new methods for PCR-free virus nucleic acid detection has been identified as the key priorities in addressing “major global health challenges”. , In recent years, a series of novel PCR-free virus nucleic acid detection methods have been developed, such as surface-enhanced Raman spectroscopy, , mass spectrometry, , fluorescence spectroscopy, , field-effect transistors, and other techniques. , All of these technologies have greatly promoted the development of nucleic acid detection technologies. However, few of these methods have been reported to be applied to the detection of viruses exposed to real environments.…”