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So far, wastewater sampling has retrospectively shown that virus is present in cities several months before large COVID-19 outbreaks,
that there is a correlation between quantitative RT-PCR data and the reported incidence of cases,
and that the presence of SARS-CoV-2 in wastewater is ubiquitous.
There are numerous benefits of wastewater sampling, but the collection and interpretation of data is an emerging field. Within the Global Polio Eradication Initiative, wastewater sampling has successfully been used to detect polioviruses and inform eradication for several decades.
This virological analysis and investigation of wastewater has been done by the Global Polio Laboratory Network and independent laboratories. Here, we highlight several challenges of wastewater sampling for SARS-CoV-2 and outline lessons that can be learnt from polio eradication.
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meaning that whether stool is a source of new infections is unclear.
can all affect sample quality, which might influence the ability to detect and isolate virus. The method of sampling (eg, 24-h composite samples vs periodic grab samples), population demographics of the catchment area, and local epidemiological factors are important for planning environmental surveillance. The method and volume of sample is also important: several approaches (eg, bag filtration and composite sampling) are used to increase the volume of a sample.
Although large sample volumes might increase identification of virus in wastewater, this can make samples increasingly intractable to handle and process in laboratories. Wastewater sampling in cities requires good maps of sewer networks to understand what population is being represented. In very mobile populations (exemplified in Pakistan) sampling might indicate the presence of virus but not the affected population. Outside of dense populations there are fewer converging sewer networks that enable informative wastewater sampling; alternative sampling strategies for remote settings are a recognised need.
Suitable process controls should be defined to validate results, identify false negatives, and minimise cross-contamination. In polio surveillance, isolation of the related non-polio enteroviruses (a group of ubiquitous enteric viruses) has been a useful quality indicator for field samples and testing performance. WHO protocols suggest that at least 10–30% of samples should reveal non-polio enteroviruses, and sites can be rejected if isolation is not possible. A clear separation in sample handling and processing is needed to reduce the risk of cross-contamination. Generally, samples are processed within biosafety level two laboratory conditions, separate from clinical samples, where the standard process involves a two-phase separation procedure (for virus concentration), followed by virus culture and isolation, as well as molecular methods that offer genome detection. Increasingly, specialist laboratories are also adopting modern sequence-based methods for wastewater surveillance, such as metagenomics or nanopore sequencing,
which generates high-resolution genomic information that offers detailed insights into possible virus origins.
Despite the challenges, wastewater sampling has long been an important supplement to clinical surveillance in polio eradication and has the potential to inform the epidemiology of COVID-19. Wastewater sampling can act as an early warning system for local infection, and support clinical surveillance to confirm local elimination through negative samples. To be an informative mode of surveillance, it will be essential to set minimum criteria for surveillance sites, develop a consistent sampling strategy, establish laboratory testing protocols to enhance sensitivity and minimise the risks of cross-contamination, and to collaborate internationally.
We declare no competing interests.
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