Detection of prevalent SARS-CoV-2 variant lineages in wastewater and clinical sequences from cities in Québec, Canada

Abstract

Wastewater-based epidemiology has emerged as a promising tool to monitor pathogens in a population, particularly when clinical diagnostic capacities become overwhelmed. During the ongoing COVID-19 pandemic caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), several jurisdictions have tracked viral concentrations in wastewater to inform public health authorities. While some studies have also sequenced SARS-CoV-2 genomes from wastewater, there have been relatively few direct comparisons between viral genetic diversity in wastewater and matched clinical samples from the same region and time period. Here we report sequencing and inference of SARS-CoV-2 mutations and variant lineages (including variants of concern) in 936 wastewater samples and thousands of matched clinical sequences collected between March 2020 and July 2021 in the cities of Montreal, Quebec City, and Laval, representing almost half the population of the Canadian province of Quebec. We benchmarked our sequencing and variant-calling methods on known viral genome sequences to establish thresholds for inferring variants in wastewater with confidence. We found that variant frequency estimates in wastewater and clinical samples are correlated over time in each city, with similar dates of first detection. Across all variant lineages, wastewater detection is more concordant with targeted outbreak sequencing than with semi-random clinical swab sampling. Most variants were first observed in clinical and outbreak data due to higher sequencing rate. However, wastewater sequencing is highly efficient, detecting more variants for a given sampling effort. This shows the potential for wastewater sequencing to provide useful public health data, especially at places or times when sufficient clinical sampling is infrequent or infeasible.

SARS-CoV-2 evolution in the absence of selective immune pressures, results in antibody resistance, interferon suppression and phenotypic differences by lineage

“…Following sequencing, the reads from each sample were used to call variants using Freebayes v1.3.6 (19) and the results were saved as a VCF file which was used to compare genomic variation across passages. Others have called variants with other tools such as DeepSNV (20) and VarScan (21). DeepSNV was not used as it only investigates SNVs (22), when indels have been found to confer selective advantages (23).…”

Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data

“…A preliminary pipeline devised to analyse wastewater sequences from variant lineages during WBS in Québec early during the pandemic (between March 2020 and July 2021 [30]). The pipeline is composed of two components: variant calling of singlenucleotide variants that pass coverage and quality thresholds, followed by post-variant-calling analysis.…”

“…Our goal was to assess how each tool performs lineage identification and quantification of mixtures of SARS-CoV-2 lineages, as would be found in wastewater, in comparison to a 'Basic' approach. The Basic approach was a preliminary attempt that showed promise in the deconvolution of lineages from wastewater samples before the development of more sophisticated tools [30], highlighting the progress that has been made since. We used simulated wastewater samples, and while true wastewater samples likely contain more diverse mixtures than simulated here, we believe our study provides a logical foundation for more complex benchmarking.…”

Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data

“…The variant calling step was run with default parameters: minimum coverage of 50x and a conservative minimum allele frequency of 25% based on findings previously reported 30 . Post-variant-calling was modified for this benchmark to include BA.1, BA.2, and BA.3, not included in the original pipeline, and updated the mutation prevalence file built using multiple-sequence-alignment on all genomes.…”

“…Basic: A pipeline devised to analyse wastewater sequences from variant lineages during WBS in Québec between March 2020 and July 2021 30 . The pipeline is composed of two components: variant calling of single nucleotide variants that pass coverage and quality thresholds, followed by post-variant-calling analysis.…”