Monitoring SARS-CoV-2 Circulation and Diversity through Community Wastewater Sequencing, the Netherlands and Belgium

Ray Izquierdo-Lara, Goffe Elsinga, Leo Heijnen, Bas B Oude Munnink, Claudia M E Schapendonk, David Nieuwenhuijse, Matthijs Kon, Lu Lu, Frank M Aarestrup, Samantha Lycett, Gertjan Medema, Marion P G Koopmans, Miranda de Graaf

Research output: Contribution to journalArticlepeer-review

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly become a major global health problem, and public health surveillance is crucial to monitor and prevent virus spread. Wastewater-based epidemiology has been proposed as an addition to disease-based surveillance because virus is shed in the feces of ≈40% of infected persons. We used next-generation sequencing of sewage samples to evaluate the diversity of SARS-CoV-2 at the community level in the Netherlands and Belgium. Phylogenetic analysis revealed the presence of the most prevalent clades (19A, 20A, and 20B) and clustering of sewage samples with clinical samples from the same region. We distinguished multiple clades within a single sewage sample by using low-frequency variant analysis. In addition, several novel mutations in the SARS-CoV-2 genome were detected. Our results illustrate how wastewater can be used to investigate the diversity of SARS-CoV-2 viruses circulating in a community and identify new outbreaks.

Original languageEnglish
Pages (from-to)1405-1415
Number of pages11
JournalEmerging Infectious Diseases
Volume27
Issue number5
Early online date31 Mar 2021
DOIs
Publication statusE-pub ahead of print - 31 Mar 2021

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