Monitoring SARS-CoV-2 variants alterations in Nice neighborhoods by wastewater nanopore sequencing

Abstract

Background Wastewater surveillance was proposed as an epidemiological tool to define the prevalence and evolution of the SARS-CoV-2 epidemics. However, most implemented SARS-CoV-2 wastewater surveillance projects were based on qPCR measurement of virus titers and did not address the mutational spectrum of SARS-CoV-2 circulating in the population. Methods We have implemented a nanopore RNA sequencing monitoring system in the city of Nice (France, 550,000 inhabitants). Between October 2020 and March 2021, we monthly analyzed the SARS-CoV-2 variants in 113 wastewater samples collected in the main wastewater treatment plant and 20 neighborhoods. Findings We initially detected the lineages predominant in Europe at the end of 2020 (B.1.160, B.1.177, B.1.367, B.1.474, and B.1.221). In January, a localized emergence of a variant (Spike:A522S) of the B.1.1.7 lineage occurred in one neighborhood. It rapidly spread and became dominant all over the city. Other variants of concern (B.1.351, P.1) were also detected in some neighborhoods, but at low frequency. Comparison with individual clinical samples collected during the same week showed that wastewater sequencing correctly identified the same lineages as those found in COVID-19 patients. Interpretation Wastewater sequencing allowed to document the diversity of SARS-CoV-2 sequences within the different neighborhoods of the city of Nice. Our results illustrate how sequencing of sewage samples can be used to track pathogen sequence diversity in the current pandemics and in future infectious disease outbreaks. Translation For the French translation of the abstract see Supplementary Materials section.

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

“…The emergent genotypes are difficult to distinguish from spuriously predicted haplotypes. Coupled approaches with Illumina short-read and Oxford Nanopore-based long-read sequencing data have greater potential to allow for the reconstruction of full-length haplotypes from mixed samples [28,45].…”

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 ).…”

“…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 ). These studies also evidenced that improvement on sequencing techniques must be performed in order to reduce error rates, as the case of Nanopore sequencing ( Nemudryi et al, 2020 ).…”

A State-of-the-Art Scoping Review on SARS-CoV-2 in Sewage Focusing on the Potential of Wastewater Surveillance for the Monitoring of the COVID-19 Pandemic

“…Also, SARS-CoV-2 VOCs have been detected in sewage (pango lineage B.1.1.7 and P.1), suggesting that tracking SARS-CoV-2 variants and their abundance in sewersheds could provide an early warning system for the emergence or spread of more infectious or virulent strains in the community. More recently, SARS-CoV-2 VOCs and VOIs were identified in wastewater samples matching those found in clinical isolates from the same time periods (Ai et al, 2021;Avgeris et al, 2021;Carcereny et al, 2021;Gregory et al, 2021;Heijnen et al, 2021;La Rosa et al, 2021c;Lee et al, 2021;Mishra et al, 2021;Rios et al, 2021;Swift et al, 2021;Wurtz et al, 2021;Yaniv et al, 2021).…”