Tracking SARS-CoV-2 in sewage: Evidence of changes in virus variant predominance during COVID-19 pandemic

Javier Martin*, Dimitra Klapsa, Thomas Wilton, Maria Zambon, Emma Bentley, Erika Bujaki, Martin Fritzsche, Ryan Mate, Manasi Majumdar

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

41 Citations (Scopus)


Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), responsible for the ongoing coronavirus disease (COVID-19) pandemic, is frequently shed in faeces during infection, and viral RNA has recently been detected in sewage in some countries. We have investigated the presence of SARS-CoV-2 RNA in wastewater samples from South-East England between 14th January and 12th May 2020. A novel nested RT-PCR approach targeting five different regions of the viral genome improved the sensitivity of RT-qPCR assays and generated nucleotide sequences at sites with known sequence polymorphisms among SARS-CoV-2 isolates. We were able to detect co-circulating virus variants, some specifically prevalent in England, and to identify changes in viral RNA sequences with time consistent with the recently reported increasing global dominance of Spike protein G614 pandemic variant. Low levels of viral RNA were detected in a sample from 11th February, 3 days before the first case was reported in the sewage plant catchment area. SARS-CoV-2 RNA concentration increased in March and April, and a sharp reduction was observed in May, showing the effects of lockdown measures. We conclude that viral RNA sequences found in sewage closely resemble those from clinical samples and that environmental surveillance can be used to monitor SARS-CoV-2 transmission, tracing virus variants and detecting virus importations.

Original languageEnglish
Article number1144
Issue number10
Publication statusPublished - Oct 2020

Bibliographical note

Funding Information:
Funding: This paper is based on independent research commissioned and funded by the National Institute for Health Research (NIHR) Policy Research Programme (NIBSC Regulatory Science Research Unit). The views expressed in the publication are those of the author(s) and not necessarily those of the NHS, the NIHR, the Department of Health, arm’s length bodies, or other government departments.

Publisher Copyright:
© 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (

Copyright 2020 Elsevier B.V., All rights reserved.


  • Alter surveillance system
  • COVID-19
  • Next-generation sequencing
  • SARS-CoV-2 RNA
  • Variant G614
  • Virus evolution
  • Wastewater


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