FN Archimer Export Format PT J TI SARS-CoV-2 Whole-Genome Sequencing Using Oxford Nanopore Technology for Variant Monitoring in Wastewaters BT AF BARBE, Laure SCHAEFFER, Julien BESNARD, Alban JOUSSE, Sarah Wurtzer, Sébastien Moulin, Laurent LE GUYADER, Soizick DESDOUITS, Marion AS 1:1;2:1;3:1;4:1;5:2;6:2;7:1;8:1; FF 1:PDG-RBE-MASAE-LSEM;2:PDG-RBE-MASAE-LSEM;3:PDG-RBE-SGMM-LSEM;4:PDG-RBE-SGMM-LSEM;5:;6:;7:PDG-RBE-MASAE-LSEM;8:PDG-RBE-MASAE-LSEM; C1 Laboratoire de Microbiologie (LSEM, Unité MASAE), IFREMER, Nantes, France R&D Laboratory, DRDQE, Eau de Paris, Ivry-sur-Seine, France C2 IFREMER, FRANCE EAU PARIS, FRANCE SI NANTES SE PDG-RBE-MASAE-LSEM PDG-RBE-SGMM-LSEM IN WOS Ifremer UPR DOAJ copubli-france IF 5.2 TC 15 AC OBEPINE Consortium UR https://archimer.ifremer.fr/doc/00775/88715/94419.pdf https://archimer.ifremer.fr/doc/00775/88715/94420.docx LA English DT Article DE ;SARS-CoV-2;variant of concern;wastewater-based epidemiology;next-generation sequencing;Oxford Nanopore Technology;sewage;ARTIC AB Since the beginning of the Coronavirus Disease-19 (COVID-19) pandemic, multiple Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) mutations have been reported and led to the emergence of variants of concern (VOC) with increased transmissibility, virulence or immune escape. In parallel, the observation of viral fecal shedding led to the quantification of SARS-CoV-2 genomes in wastewater, providing information about the dynamics of SARS-CoV-2 infections within a population including symptomatic and asymptomatic individuals. Here, we aimed to adapt a sequencing technique initially designed for clinical samples to apply it to the challenging and mixed wastewater matrix, and hence identify the circulation of VOC at the community level. Composite raw sewage sampled over 24 h in two wastewater-treatment plants (WWTPs) from a city in western France were collected weekly and SARS-CoV-2 quantified by RT-PCR. Samples collected between October 2020 and May 2021 were submitted to whole-genome sequencing (WGS) using the primers and protocol published by the ARTIC Network and a MinION Mk1C sequencer (Oxford Nanopore Technologies, Oxford, United Kingdom). The protocol was adapted to allow near-full genome coverage from sewage samples, starting from ∼5% to reach ∼90% at depth 30. This enabled us to detect multiple single-nucleotide variant (SNV) and assess the circulation of the SARS-CoV-2 VOC Alpha, Beta, Gamma, and Delta. Retrospective analysis of sewage samples shed light on the emergence of the Alpha VOC with detection of first co-occurring signature mutations in mid-November 2020 to reach predominance of this variant in early February 2021. In parallel, a mutation-specific qRT-PCR assay confirmed the spread of the Alpha VOC but detected it later than WGS. Altogether, these data show that SARS-CoV-2 sequencing in sewage can be used for early detection of an emerging VOC in a population and confirm its ability to track shifts in variant predominance. PY 2022 PD JUL SO Frontiers In Microbiology SN 1664-302X PU Frontiers Media VL 13 UT 000815002200001 DI 10.3389/fmicb.2022.889811 ID 88715 ER EF