Reader TTS

Methods for monitoring wastewater for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and emerging variants have risen to prominence during the COVID-19 pandemic. Routine

monitoring of wastewater should be deployed around the world to mitigate the spread of pathogens, both old and new. In late June 2022, wastewater surveillance in London, UK, identified

poliovirus on consecutive occasions, which indicated a provisional outbreak and prompted health officials to instigate catch-up vaccination campaigns to prevent infections in the

unvaccinated that can lead to paralysis in some cases (less than 5 out of every 1,000 people infected). For years, wastewater monitoring has been routinely implemented in many regions as an

early warning system to identify and rapidly mitigate the spread of many pathogens, including norovirus, hepatitis viruses and salmonella — and more recently SARS-CoV-2 — in addition to

poliovirus. In the UK, the last case of wild polio was reported in 1984, and the UK was declared polio-free in 2003. By 2020, most of the world was considered by health agencies to be

poliovirus-free. Such declarations belie the complexities of viral epidemiology and the global inequalities in public health. In Pakistan and Afghanistan, for example, poliovirus is still

endemic, and there are numerous other countries where poliovirus routinely circulates. As long as poliovirus is found anywhere, it is a potential problem everywhere. As the recent outbreak

in London highlights, even regions where disease is unlikely owing to high rates of vaccination should maintain vigilance in screening and immunization efforts. There are two vaccines used

against poliovirus today, each of which has pros and cons. The oral polio vaccine (OPV) is a live attenuated virus vaccine that is used across much of the developing world. Although the OPV

prevents disease and transmission, the weakened virus can, very rarely, revert to a neurovirulent form referred to as vaccine-derived poliovirus (VDPV), which has the potential to spread and

lead to infections that result in paralysis. The other vaccine, the inactivated polio vaccine (IPV), is used in higher-income countries. It confers strong protection against disease without

the risk of reversion, but it does not prevent transmission. Like most high-income countries, the UK exclusively administers the IPV today. Investigation of the outbreak detected in June

indicated that the virus found in sewage samples was VDPV, likely brought to London by people who had been previously vaccinated by the OPV in another country. Although such transmission

does not pose a threat to anyone who is vaccinated, it puts those who are vulnerable, such as children too young to be fully immunized, at risk of infection. One way to detect polioviruses

that are spreading without causing symptoms in regions declared free of the virus is through epidemiological surveillance of wastewater. At wastewater treatment facilities, sewage from an

entire region is combined, such that culturing, PCR or metagenomics-based sampling of a single wastewater sample can detect the presence of pathogens at the population level. What this

approach lacks in terms of individual patient-level specificity, it makes up for by sampling large swathes of the population. Perhaps more importantly, this approach can detect the presence

of circulating pathogens before patients present to clinicians with symptoms, thereby giving public-health experts time to mount defences before outbreaks occur. Accurate detection of

viruses from wastewater samples can be challenging1. Larger quantities of sewage sludge are typically filtered to remove debris, before viruses can be concentrated through filtration

techniques, flocculation, precipitation or centrifugation. Concentration techniques can damage genomic material or cause the build-up of substances that inhibit molecular analyses like PCR.

Sewage also contains an abundance of other microbes and viruses that can confound results or lead to false positives, as well as human DNA, which in turn raises concerns about privacy.

Despite these challenges, wastewater surveillance has been instrumental in controlling past outbreaks of poliovirus. Between 2013–2014, after 25 years without a case, Israel detected wild

poliovirus in wastewater samples. More recently, in March 2022, poliovirus was detected in sewage samples from Jerusalem and surrounding regions. In both instances, the authorities dealt

with the outbreaks with campaigns to vaccinate those not already fully immunized, which curtailed further spread of the virus. Rapid detection enabled by wastewater surveillance was crucial

to stop the disease caused by poliovirus: in the 2013–2014 outbreak in Israel there were no cases of paralysis, and in 2022, there was only one case of paralysis in an unvaccinated child.

Similarly, after the recent outbreak in London, increased public messaging about poliovirus and vaccination schedules in children, many of whom have fallen behind as a result of the COVID-19

pandemic, has thus far prevented any cases of paralysis. For an ongoing and rapidly evolving pandemic such as that of COVID-19, wastewater surveillance2,3 can be used both to detect the

presence or absence of the virus, as well as the emergence and transmission of new variants that are more transmissible or immune-evading. SARS-CoV-2 variant detection necessitates

pinpointing low-abundance, subtly different genomes from amidst a confounding mix of genomic material. In this issue of _Nature Microbiology_, Jahn and co-authors report a bioinformatics

method named Co-Occurrence adJusted Analysis and Calling (COJAC) that detected the local spread of Alpha, Beta and Gamma variants in SARS-CoV-2 RNA amplicon sequencing from wastewater

samples in two cities in Switzerland. COJAC scans for read pairs with multiple variant-specific mutations to enable detection. Similarly, reporting in _Nature_, Karthikeyan and co-authors

describe an optimized approach for the concentration of viruses from wastewater, and software for variant deconvolution informed by high-resolution, long-term clinical and wastewater

sequencing4. Their tool, called Freyja, uses a library of single-nucleotide-variant frequencies as molecular barcodes for each lineage of SARS-CoV-2 in the global phylogeny and detects

variants from SARS-CoV-2 RNA amplicon sequencing. Both tools rely on databases of known variants, so neither has yet been used to detect the emergence of new variants of concern. There are

additional limitations to approaches for wastewater surveillance for SARS-CoV-2 and other pathogens. While treatment plants can report back on pathogens present in millions of people via

wastewater collection, this type of surveillance is a blunt instrument. Wastewater surveillance cannot pinpoint infected individuals, transmission, or account for the interconnectedness of

modern society or the mobility of the populations in any given region. Infected people could merely be passing through, unwittingly spreading a pathogen and confounding wastewater detection

efforts, because the index case might have moved on from a region by the time the pathogen is detected. The drawbacks of wastewater surveillance are offset by the foresight that approaches

such as COJAC and Freyja provide. Both methods detected outbreaks more than two weeks before the first positive clinical tests were reported. Another advantage is that wastewater

surveillance is more economical than clinical testing: it effectively screens large numbers of people in just a few samples, and doesn’t require clinician-led sampling. Wastewater

surveillance is not just for viruses. It can be used to detect other microbial pathogens5, antimicrobial resistance6, or chemical water contaminants7. Furthermore, these tools are not

limited to wastewater treatment facilities, and could be applied to samples from other settings such as transport hubs, hospitals, schools, workplaces and leisure facilities8. Apart from

public-health applications, the data generated by wastewater surveillance might be useful for researchers investigating community trends and the efficacy of health policies and

non-pharmaceutical interventions. To enable implementation of public-health measures as soon as they are needed, and to intervene against the spread of infectious disease, any strategy that

enables economical, early and efficient detection is key, and these methods seem to fit the bill. Wastewater surveillance is poised to become embedded in public-health strategies across the

globe — at least 55 countries9 track SARS-CoV-2 in wastewater already — but it needs to be shown to be practical and informative in both high- and low-income countries. This is especially

true for regions without ready access to COVID-19 vaccines, so as to prevent against new waves of variant infection, because unchecked transmission anywhere is a problem everywhere.

REFERENCES * Farkas, K., Hillary, L. S., Malham, S. K., McDonald, J. E. & Jones, D. L. _Curr. Opin. Environ. Sci. Health_ 17, 14–20 (2020). Article  Google Scholar  * Vogel, G. _Science_

https://doi.org/10.1126/science.adb1932 (2022). Article  PubMed  Google Scholar  * Schmidt, C. _Nat. Biotechnol._ 38, 917–920 (2020). Article  Google Scholar  * Karthikeyan, S. et al.

_Nature_ https://doi.org/10.1038/s41586-022-05049-6 (2022). Article  PubMed  Google Scholar  * Ko, K. K. K., Chng, K. R. & Nagarajan, N. _Nat. Microbiol._ 7, 486–496 (2022). Article  CAS

  Google Scholar  * Hendriksen, R. S. et al. _Nat. Commun._ 10, 1124 (2019). Article  Google Scholar  * Jung, J. K. et al. _Nat. Biotechnol._ 38, 1451–1459 (2020). Article  CAS  Google

Scholar  * Nordahl Petersen, T. et al. _Sci. Rep._ 5, 11444 (2015). Article  Google Scholar  * Ahmed, W. et al. _Sci. Total Environ._ 805, 149877 (2022). Article  CAS  Google Scholar 

Download references RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Wastewater monitoring comes of age. _Nat Microbiol_ 7, 1101–1102 (2022).

https://doi.org/10.1038/s41564-022-01201-0 Download citation * Published: 02 August 2022 * Issue Date: August 2022 * DOI: https://doi.org/10.1038/s41564-022-01201-0 SHARE THIS ARTICLE Anyone

you share the following link with will be able to read this content: Get shareable link Sorry, a shareable link is not currently available for this article. Copy to clipboard Provided by

the Springer Nature SharedIt content-sharing initiative