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Metagenomic sequencing of municipal wastewater provides a near-complete SARS-CoV-2 genome sequence identified as the B.1.1.7 variant of concern from a Canadian municipality concurrent with an outbreak
Chrystal Landgraff; Lu Ya Ruth Wang; Cody Buchanan; Matthew Wells; Justin Schonfeld; Kyrylo Bessonov; Jennifer Ali; Erin Robert; Celine Nadon.
Afiliação
  • Chrystal Landgraff; Public Health Agency of Canada
  • Lu Ya Ruth Wang; Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada
  • Cody Buchanan; Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada
  • Matthew Wells; Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada
  • Justin Schonfeld; Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada
  • Kyrylo Bessonov; Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada
  • Jennifer Ali; Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada
  • Erin Robert; Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada
  • Celine Nadon; Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada and Department of Medical Microbiology and Infectious Diseases, M
Preprint em Inglês | medRxiv | ID: ppmedrxiv-21253409
ABSTRACT
Laboratory-based wastewater surveillance for SARS-CoV-2, the causative agent of the ongoing COVID-19 pandemic, can be conducted using RT-qPCR-based screening of municipal wastewater samples. Although it provides rapid viral detection and can inform SARS-CoV-2 abundance in wastewater, this approach lacks the resolution required for viral genotyping and does not support tracking of viral genome evolution. The recent emergence of several variants of concern, a result of mutations across the genome including the accrual of important mutations within the viral spike glycoprotein, has highlighted the need for a method capable of detecting the cohort of mutations associated with these and newly emerging genotypes. Here we provide an innovative methodology for the recovery of a near-complete SARS-CoV-2 sequence from a wastewater sample collected from across Canadian municipalities including one that experienced a significant outbreak attributable to the SARS-CoV-2 B.1.1.7 variant of concern. Our results demonstrate that a combined interrogation of genome consensus-level sequences and alternative alleles enables the identification of a SARS-CoV-2 variant of concern and the detection of a new allele within a viral accessory gene that may be representative of a recently evolved B.1.1.7 sublineage.
Licença
cc_by_nc_nd
Texto completo: Disponível Coleções: Preprints Base de dados: medRxiv Tipo de estudo: Cohort_studies / Estudo diagnóstico / Estudo observacional / Estudo prognóstico Idioma: Inglês Ano de publicação: 2021 Tipo de documento: Preprint
Texto completo: Disponível Coleções: Preprints Base de dados: medRxiv Tipo de estudo: Cohort_studies / Estudo diagnóstico / Estudo observacional / Estudo prognóstico Idioma: Inglês Ano de publicação: 2021 Tipo de documento: Preprint
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