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Article

Tracking SARS-CoV-2 in Sewage: Evidence of Changes in Virus Variant Predominance during COVID-19 Pandemic

1
Division of Virology, National Institute for Biological Standards and Control (NIBSC), Potters Bar, Hertfordshire EN6 3QG, UK
2
Respiratory Virology & Polio Reference Service, Public Health England, London NW9 5EQ, UK
3
Division of Analytical and Biological Sciences, NIBSC, Potters Bar, Hertfordshire EN6 3QG, UK
*
Author to whom correspondence should be addressed.
Received: 25 September 2020 / Revised: 2 October 2020 / Accepted: 4 October 2020 / Published: 9 October 2020
(This article belongs to the Collection Coronaviruses)
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. View Full-Text
Keywords: COVID-19; wastewater; SARS-CoV-2 RNA; next-generation sequencing; variant G614; virus evolution; alter surveillance system COVID-19; wastewater; SARS-CoV-2 RNA; next-generation sequencing; variant G614; virus evolution; alter surveillance system
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MDPI and ACS Style

Martin, J.; Klapsa, D.; Wilton, T.; Zambon, M.; Bentley, E.; Bujaki, E.; Fritzsche, M.; Mate, R.; Majumdar, M. Tracking SARS-CoV-2 in Sewage: Evidence of Changes in Virus Variant Predominance during COVID-19 Pandemic. Viruses 2020, 12, 1144. https://0-doi-org.brum.beds.ac.uk/10.3390/v12101144

AMA Style

Martin J, Klapsa D, Wilton T, Zambon M, Bentley E, Bujaki E, Fritzsche M, Mate R, Majumdar M. Tracking SARS-CoV-2 in Sewage: Evidence of Changes in Virus Variant Predominance during COVID-19 Pandemic. Viruses. 2020; 12(10):1144. https://0-doi-org.brum.beds.ac.uk/10.3390/v12101144

Chicago/Turabian Style

Martin, Javier; Klapsa, Dimitra; Wilton, Thomas; Zambon, Maria; Bentley, Emma; Bujaki, Erika; Fritzsche, Martin; Mate, Ryan; Majumdar, Manasi. 2020. "Tracking SARS-CoV-2 in Sewage: Evidence of Changes in Virus Variant Predominance during COVID-19 Pandemic" Viruses 12, no. 10: 1144. https://0-doi-org.brum.beds.ac.uk/10.3390/v12101144

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