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.
Highlights
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has dramatically affected all countries worldwide
The major lineages in circulation, determined from clinical samples, during October 2020 were B.1.221, B.1.160, or B.1.177, while from the end of December 2020 B.1.1.7 and B.1.351 was detected at increasing numbers and B.1.1.7 became the dominant lineage by the end of January 2021 (Figure S2 in Supplementary Material)
Genomic sequencing of SARS-CoV-2 from wastewater has the potential to be a valuable tool in population-wide monitoring of circulating lineages
Summary
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has dramatically affected all countries worldwide. In Luxembourg, the first SARS-CoV-2 positive case was identified on 29 February 2020, marking the beginning of the national genomic surveillance by sequencing. While SARS-CoV-2 is primarily transmitted through aerosols [2], the virus can persistently be detected in the urine and feces of infected people [3,4,5]. The presence of this virus in the excreta of infected patients led researchers to question its transmission through the water cycle and its persistence in the environment [6,7,8]. Further evaluation is required in terms of transmissibility [15] or stability [16] of SARS-CoV-2 in effluents, wastewaterbased surveillance emerged as a valuable monitoring tool [17,18] with the potential to mitigate delays of individual testing [11]
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