Genome Sequencing of SARS-CoV-2 Allows Monitoring of Variants of Concern through Wastewater

Abstract

Monitoring SARS-CoV-2 in wastewater has shown to be an effective tool for epidemiological surveillance. More specifically, RNA levels determined with RT-qPCR have been shown to track with the infection dynamics within the population. However, the surveillance of individual lineages circulating in the population based on genomic sequencing of wastewater samples is challenging, as the genetic material constitutes a mixture of different viral haplotypes. Here, we identify specific signature mutations from individual SARS-CoV-2 lineages in wastewater samples to estimate lineages circulating in Luxembourg. We compare circulating lineages and mutations to those detected in clinical samples amongst infected individuals. We show that especially for dominant lineages, the allele frequencies of signature mutations correspond to the occurrence of particular lineages in the population. In addition, we provide evidence that regional clusters can also be discerned. We focused on the time period between November 2020 and March 2021 in which several variants of concern emerged and specifically traced the lineage B.1.1.7, which became dominant in Luxembourg during that time. During the subsequent time points, we were able to reconstruct short haplotypes, highlighting the co-occurrence of several signature mutations. Our results highlight the potential of genomic surveillance in wastewater samples based on amplicon short-read data. By extension, our work provides the basis for the early detection of novel SARS-CoV-2 variants.

Spatial and temporal distribution of SARS-CoV-2 diversity circulating in wastewater

“…Massive parallel sequencing techniques applied to sewage samples allow us to analyze a large number of SARS-CoV-2 genomes, including those present in symptomatic and asymptomatic persons. Through the analysis of sequences, it is possible to detect low-frequency variants (LFV) and to infer which lineages are circulating at a certain time and place ( Bar-Or et al, 2021 ; Crits-Christoph et al, 2021 ; Dharmadhikari et al, 2021 ; Herold et al, 2021 ; Izquierdo-Lara et al, 2021 ; La Rosa et al, 2021 ; Nemudryi et al, 2020 ; Rios et al, 2021 ). Additionally, genomic analyses may allow to detect the entry of described lineages or Variants of Concern (VOCs) into populations, as well as the appearance of emerging lineages, to characterize new outbreaks, and to aid in viral strains tracking ( Bar-Or et al, 2021 ; Crits-Christoph et al, 2021 ; Izquierdo-Lara et al, 2021 ; La Rosa et al, 2021 ; Nemudryi et al, 2020 ; Rios et al, 2021 ).…”

QuaID: Enabling Earlier Detection of Recently Emerged SARS-CoV-2 Variants of Concern in Wastewater

“…Wastewater monitoring is an invaluable tool for SARS-CoV-2 surveillance [1][2][3][4][5][6][7][8] . Despite multiple recent successes in VoC monitoring and detection from wastewater sequencing data [9][10][11][12][13][14][15] , there are multiple challenges associated with the nature of the environmental data.…”

“…Despite multiple recent successes in VoC monitoring and detection from wastewater sequencing data [9][10][11][12][13][14][15] , there are multiple challenges associated with the nature of the environmental data. Since wastewater represents a pooled sample of multiple hosts, it harbors a diversity of SARS-CoV-2 variants that are currently circulating in the population 1,2,10,13 , including potentially previously unreported genotypes 16 . Furthermore, variant detection and phasing is further complicated by uneven genome coverage 2,17,18 and environmental RNA degradation 5,19,20 which render phased assembly extremely difficult [21][22][23] .…”

Metagenomics of Wastewater Influent from Wastewater Treatment Facilities across Ontario in the Era of Emerging SARS-CoV-2 Variants of Concern

“…SARS-CoV-2 is shed in human fecal matter and less so in urine by infected individuals, and its detection in wastewater triggered global interest in tracking the dissemination of its VOCs ( 3 , 4 ). The province of Ontario and other jurisdictions have adopted genomic surveillance of wastewater for monitoring known and emerging SARS-CoV-2 VOCs in the community ( 5 – 12 ).…”