Genomic surveillance of Canadian airport wastewater samples allows early detection of emerging SARS-CoV-2 lineages

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has shown wastewater (WW) surveillance to be an effective means of tracking the emergence of viral lineages which arrive by many routes of transmission including via transportation hubs. In the Canadian province of Ontario, numerous municipal wastewater treatment plants (WWTPs) participate in WW surveillance of infectious disease targets such as SARS-CoV-2 by qPCR and whole genome sequencing (WGS). The Greater Toronto Airports Authority (GTAA), operator of Toronto Pearson International Airport (Toronto Pearson), has been participating in WW surveillance since January 2022. As a major international airport in Canada and the largest national hub, this airport is an ideal location for tracking globally emerging SARS-CoV-2 variants of concern (VOCs). In this study, WW collected from Toronto Pearson's two terminals and pooled aircraft sewage was processed for WGS using a tiled-amplicon approach targeting the SARS-CoV-2 virus genome. Data generated was analyzed to monitor trends of SARS-CoV-2 lineage frequencies. Initial detections of emerging lineages were compared between Toronto Pearson WW samples, municipal WW samples collected from the surrounding regions, and Ontario clinical data as published by Public Health Ontario. Results enabled the early detection of VOCs and individual mutations emerging in Ontario. On average, the emergence of novel lineages at the airport preceded clinical detections by 1-4 weeks, and up to 16 weeks in one case. This project illustrates the efficacy of WW surveillance at transitory transportation hubs and sets an example that could be applied to other viruses as part of a pandemic preparedness strategy and to provide monitoring on a mass scale.

Fig. 1

Map of sewersheds and sampling sites in the regions surrounding Pearson Airport.

Fig. 2

Frequency of lineages of interest from the de-mixing performed by Alcov (log sale). Horizontal dashed lines represent the 5% and 1% detection thresholds. Each point represents a single WW sample. Points with a frequency less than 1% are dimmed, as these are too low to consider a lineage as “detected”. The x-axis represents the weeks since the first PHO reported Ontario clinical case, with negative values representing detections in WW prior to clinical detections. Each panel represents a single lineage from the following list: BA.2.75* (A), BF* (B), BQ* (C), XBB.1.16* (D), XBB.1.5* (E), XBB.1.9* (F), XBB* (G).

Fig. 3

Cumulative detection probabilities for each lineage and location. Dotted lines represent detections with a 0.01 (1%) detection threshold, and solid lines represent detections with a threshold of 0.05 (5%). The x-axis represents the weeks since the first PHO reported Ontario clinical case, with negative values representing detections in WW prior to clinical detections. Each panel represents a single lineage from the following list: BA.2.75* (A), BF* (B), BQ* (C), XBB.1.16* (D), XBB.1.5* (E), XBB.1.9* (F), XBB* (G).

Fig. 4

Frequency of the alert mutation S: R346T in WW samples from Toronto Pearson and surrounding municipal sites in Toronto, York, and Peel regions. Each point represents a single WW sample.