Use of wastewater analysis to evaluate the incidence of SARS-CoV-2 in the UK population
Dr Kata Farkas
ASSAf & SAMRC webinar 31 August 2021
Wastewater-based epidemiology at Bangor University
• One-year surveillance of wastewater with monthly sampling at WWTPs around the Conwy River and estuary in North Wales in 2016-17
• Enteric virus (norovirus, sapovirus) concentration spikes in wastewater coincide with local gastroenteritis outbreaks
Farkas K, Cooper DM, McDonald JE, Malham SK, de Rougemont A, Jones DL (2018) Science of the Total Environment, 634:1174-1183
Wastewater as an integrator of the incidence of Covid- 19 within the UK population
• March 2020 – August 2020
• First wave of the pandemic
• Grab samples weekly
• Sample concentration, qPCR detection,
sequencing
Wastewater as an integrator of the incidence of Covid-19 within the UK population
• SARS-CoV-2 RNA abundance and diversity reflects clinical case load and lineages.
• Temporal analysis of SARS-CoV-2 in sewage tracks the effectiveness of lockdowns.
• Wastewater-based epidemiology is a useful tool for pandemic response policy.
• Further research is required to understand factors that affect virus quantification.
Hillary LS, Farkas K, Maher KH, Lucaci A, Thorpe J, Distaso MA, Gaze WH, Paterson S, Burke T, Connor TR, McDonald JE, Jones DL. Water Research. 2021 8:117214.
Wastewater-based community-level surveillance of COVID-19 in Wales
• Sampling 3-5 times a week at 19 locations
• September 2020 - ongoing
• Normalisation factors
• process efficiency
• population
• wastewater dilutions
• Predictive modelling: 5-14 days ahead
Wastewater-Based community-level surveillance of COVID-19 in Wales
Pellet et al., unpublished
Wade M, Lo Jacomo A, Armenise E, Brown M, Bunce J, Cameron G, Fang Z, Farkas K, Gilpin D, Graham D, Grimsley J. https://doi.org/10.1002/essoar.10507606.1
Factors affecting virus quantification
• Grab vs composite samples
• Virus decay in pipes
• Sample process
• Viral detection method
• Virus dilution
• Changing population
• Viral evolution
Farkas K, Hillary LS, Thorpe J, Walker DI, Lowther JA, McDonald JE, Malham SK, Jones DL. Methods and protocols. 2021 Mar;4(1):17.
Research objectives
• Recovery efficiency
• Best sampling strategy
• Residence times in pipes
• New variant detection and future applications
Recovery efficiency
• Concentration method: precipitation (AS) vs ultrafiltration (IP)
• Sample turbidity
• Surfactants
Use of process controls is recommended
Kevill et al., unpublished
Best sampling strategy
• Grab vs. composite
• Passive samplers
Passive samplers
• Optimal exposure time and place?
A B C D E F G H
SARS-CoV-2 (gc/ul)
0 20 40 60 80 100
A B C D E F G H
Phi-6 (gc/l)
0 500 1000 1500 2000 2500
Residence times in pipes
Flush rhodamine and enveloped
bacteriophage phi 6 (inactivated) down the pipes – sample wastewater for
detection
New variant detection
Beta Gamma Delta Kappa
April 2021 0.8%
(1/124)
1.6%
(2/124)
10.7%
(13/122)
2.5%
(3/122) May 2021 2.9%
(3/104)
10.6%
(11/104)
37.5%
(39/104)
1.0%
(1/104)
June 2021 0 5.3%
(18/341)
17.3%
(59/341) 0
July 2021 2.0%
(5/252)
9.5%
(24/252)
25.8%
(65/252) 0
Sample degradation may be an issue when archived samples are tested.
Duplex RT-qPCR assays were developed for the detection of Beta-Gamma and Delta-Kappa variants
Tested on concentrated sewage extracts (n=827)
Summary
• WBE can be useful for outbreak tracking and mitigation
• Predictive models have the potential to project outbreak dynamics
• Methods using control viruses should be carefully validated for accurate results
• Alternative sampling, for example passive samplers, methods may be useful when resources are limited
• Structure of sewage systems should be better understood
• qPCR can be useful for the rapid detection of emerging variants
Acknowledgement
Academy of Science of South Africa (ASSAf)
ASSAf Research Repository http://research.assaf.org.za/
B. Academy of Science of South Africa (ASSAf) Events I. Other
2021
Wastewater surveillance in the
Management of Covid 19: experiences from three Countries
Academy of Science of South Africa (ASSAf)
Academy of Science of South Africa (ASSAf); South African Medical Research Council (SAMRC)
Academy of Science of South Africa (ASSAf), (2021). Wastewater surveillance in the
Management of Covid 19: experiences from three Countries. [Online] Available at: http://hdl.handle.net/20.500.11911/204 https://youtu.be/xmYwipQtNcE
Downloaded from ASSAf Research Repository, Academy of Science of South Africa (ASSAf)
