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Wastewater monitoring took off during the COVID-19 pandemic – and here’s how it could help head off future outbreaks

Over 800 sites across the US report coronavirus data from sewage to the CDC. Here’s how this kind of surveillance system works and what it can and can’t…

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Sampling wastewater can be time-intensive. John Eisele/Colorado State University

A community’s sewage holds clues about its COVID-19 burden. Over the course of the pandemic, wastewater surveillance has become an increasingly popular way to try to understand local infection trends.

Microbiologists Susan De Long and Carol Wilusz met and became wastewater aficionados in April 2020 when a grassroots group of wastewater treatment plant operators asked them to develop and deploy a test to detect SARS-CoV-2 in samples from the sewers of Colorado. De Long is an environmental engineer who studies useful bacteria. Wilusz’s expertise is in RNA biology. Here they describe how wastewater surveillance works and what it could do in a post-pandemic future.

How is wastewater monitored for SARS-CoV-2?

Wastewater surveillance takes advantage of the fact that many human pathogens and products of human drug metabolism end up in urine, feces or both. The SARS-CoV-2 virus that causes COVID-19 shows up in surprisingly large quantities in feces of infected people, even though this is not a major route of disease transmission.

To figure out whether any pathogens are present, we first need to collect a representative sample of wastewater, either directly from the sewer or at the point where what engineers call “influent” enters a treatment plant. We can also use solids that have settled out of the wastewater.

Technicians then need to remove large particles of fecal matter and concentrate any microbes or viruses. The next step is extracting their nucleic acids – the DNA or RNA that holds the pathogens’ genetic information.

The sequences contained in the DNA or RNA act as unique bar codes for the pathogens present. For instance, if we detect genes that are unique to SARS-CoV-2, we know that the coronavirus is in our sample. We use PCR-based approaches, similar to those used in clinical diagnostic tests, to detect and quantify SARS-CoV-2 sequences.

masked lab worker with glassware and lab equipment
A lab technician prepares to process wastewater samples for SARS-CoV-2 detection at Colorado State University. John Eisele/Colorado State University

Characterizing the nucleic acid sequence in more detail can provide information about viral strains – for instance, it can identify variants like omicron BA.2.

Currently, the vast majority of wastewater surveillance efforts are focused on SARS-CoV-2, but the same techniques work with other pathogens, including poliovirus, influenza and noroviruses.

Before the pandemic, one application was monitoring for rare poliovirus outbreaks in areas where polio vaccination is ongoing. Wastewater can also be monitored for signs of various drugs to give insights into the level and type of drug use in a population.

Where does the data go?

During the pandemic, the U.S. Centers for Disease Control and Prevention developed the National Wastewater Surveillance System specifically to track SARS-CoV-2 across the country. Over 800 sites report data to this NWSS system, but not all states and counties are currently represented.

Map of U.S. with dots for sites that report to NWSS
More than 800 sites that cover populations of various sizes report COVID-19 wastewater numbers to the CDC. CDC COVID Data Tracker, CC BY

Many state agencies, like the Colorado Department of Public Health and Environment, and cities, like Tempe, Arizona, have their own dashboards for reporting data. Some companies performing wastewater analysis report data on their own dashboards, too.

In our opinion, the NWSS represents an exciting first step in monitoring population health through wastewater. Similar systems are being established in other countries, including Australia and New Zealand.

What does wastewater data really show?

SARS-CoV-2 levels in wastewater from large populations are an excellent indicator of the infection level in a community. The system automatically monitors everyone who lives in the sewershed, so it’s anonymous, unbiased and equitable. Importantly, it is also impossible to track the infection back to a particular person, household or neighborhood without taking additional samples.

Wastewater surveillance doesn’t rely on the availability of clinical tests or people reporting their test results. It also picks up asymptomatic and pre-symptomatic cases of COVID-19; this is critical because people who are infected but don’t feel sick can still spread COVID-19.

In our opinion, wastewater testing is increasingly important as more COVID-19 tests are done at home. And because vaccination has also led to more mild and asymptomatic cases of COVID-19, people may be infected without getting tested at all. These factors mean that clinical case data are less informative than earlier in the pandemic, while wastewater data remains a consistent indicator of community infection level.

COVID-19 rapid tests for home use on a pharmacy shelf
Wastewater surveillance doesn’t rely on people reporting a positive home test or even being aware of their infections. Spencer Platt/Getty Images News

So far, you can’t accurately predict the number of infected individuals in a community based on the level of virus in its wastewater. The stage of someone’s infection, how their body responds to the virus, the viral variant, how far a person was from where the wastewater sample was taken, even the weather can all affect the amounts of SARS-CoV-2 measured in sewage.

But scientists can infer relative changes in infection rates. Watching viral levels go up and down in sewage provides a glimpse of whether cases are rising or falling in the community as a whole.

Because SARS-CoV-2 can be detected in wastewater days or even weeks before outbreaks occur, wastewater monitoring can provide an early warning that public health measures may be warranted. And trends in the signal are important – if you know levels are rising, it may be a good time to reinstitute a mask mandate or recommend working from home. At present, public health officials use wastewater monitoring data along with other information like test positivity rates and the number of clinical cases and hospitalizations in the community to make these kinds of decisions.

Data from sequencing can also help detect new variants and monitor their levels, allowing health responses to take into account the characteristics of the variant present.

In smaller populations, such as in college dormitories and nursing homes, wastewater monitoring can detect a small number of infected people. That can sound the alarm that targeted clinical testing is in order to identify infected people for isolation. Early detection, targeted testing and quarantining are effective at preventing outbreaks. Rather than using clinical testing for routine monitoring, administrators can reserve disruptive clinical tests for times when SARS-CoV-2 is detected in the wastewater.

What will monitoring look like in the future?

Widespread and routine use of wastewater monitoring would give public health officials access to information about the levels of a range of potential infections in U.S. communities. This data could guide decisions about where to provide additional resources to communities, like holding testing or vaccination clinics in places where infection is on the rise. It could also help determine when interventions like masking or school closures are necessary.

In the best case, wastewater monitoring might catch a new virus when it first arrives in a new area; an early shutdown in the very localized area could potentially prevent a future pandemic. Interestingly, researchers have detected SARS-CoV-2 in archived wastewater samples collected before anyone had been diagnosed with COVID-19. If wastewater monitoring had been part of the established public health infrastructure back in late 2019, it could have provided an earlier warning that SARS-CoV-2 was becoming a global threat.

For now, though, establishing and operating a national wastewater surveillance system, particularly one that includes building-level monitoring at key locations, is still too costly and labor-intensive.

Ongoing research and development efforts are trying to simplify and automate wastewater sampling. On the analysis side, adaptation of PCR and sequencing technologies to detect other pathogens, including novel ones, will be vital to take full advantage of such a system. Ultimately, wastewater surveillance could help support a future in which pandemics are far less deadly and have less social and economic impact.

[Research into coronavirus and other news from science Subscribe to The Conversation’s new science newsletter.]

Susan De Long receives funding from Colorado Department of Public Health and Environment, the Anschutz Foundation, the National Science Foundation, and the Department of Energy.

Carol Wilusz receives funding from Colorado Department of Public Health & Environment and the Anschutz Foundation.

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The next pandemic? It’s already here for Earth’s wildlife

Bird flu is decimating species already threatened by climate change and habitat loss.

I am a conservation biologist who studies emerging infectious diseases. When people ask me what I think the next pandemic will be I often say that we are in the midst of one – it’s just afflicting a great many species more than ours.

I am referring to the highly pathogenic strain of avian influenza H5N1 (HPAI H5N1), otherwise known as bird flu, which has killed millions of birds and unknown numbers of mammals, particularly during the past three years.

This is the strain that emerged in domestic geese in China in 1997 and quickly jumped to humans in south-east Asia with a mortality rate of around 40-50%. My research group encountered the virus when it killed a mammal, an endangered Owston’s palm civet, in a captive breeding programme in Cuc Phuong National Park Vietnam in 2005.

How these animals caught bird flu was never confirmed. Their diet is mainly earthworms, so they had not been infected by eating diseased poultry like many captive tigers in the region.

This discovery prompted us to collate all confirmed reports of fatal infection with bird flu to assess just how broad a threat to wildlife this virus might pose.

This is how a newly discovered virus in Chinese poultry came to threaten so much of the world’s biodiversity.

H5N1 originated on a Chinese poultry farm in 1997. ChameleonsEye/Shutterstock

The first signs

Until December 2005, most confirmed infections had been found in a few zoos and rescue centres in Thailand and Cambodia. Our analysis in 2006 showed that nearly half (48%) of all the different groups of birds (known to taxonomists as “orders”) contained a species in which a fatal infection of bird flu had been reported. These 13 orders comprised 84% of all bird species.

We reasoned 20 years ago that the strains of H5N1 circulating were probably highly pathogenic to all bird orders. We also showed that the list of confirmed infected species included those that were globally threatened and that important habitats, such as Vietnam’s Mekong delta, lay close to reported poultry outbreaks.

Mammals known to be susceptible to bird flu during the early 2000s included primates, rodents, pigs and rabbits. Large carnivores such as Bengal tigers and clouded leopards were reported to have been killed, as well as domestic cats.

Our 2006 paper showed the ease with which this virus crossed species barriers and suggested it might one day produce a pandemic-scale threat to global biodiversity.

Unfortunately, our warnings were correct.

A roving sickness

Two decades on, bird flu is killing species from the high Arctic to mainland Antarctica.

In the past couple of years, bird flu has spread rapidly across Europe and infiltrated North and South America, killing millions of poultry and a variety of bird and mammal species. A recent paper found that 26 countries have reported at least 48 mammal species that have died from the virus since 2020, when the latest increase in reported infections started.

Not even the ocean is safe. Since 2020, 13 species of aquatic mammal have succumbed, including American sea lions, porpoises and dolphins, often dying in their thousands in South America. A wide range of scavenging and predatory mammals that live on land are now also confirmed to be susceptible, including mountain lions, lynx, brown, black and polar bears.

The UK alone has lost over 75% of its great skuas and seen a 25% decline in northern gannets. Recent declines in sandwich terns (35%) and common terns (42%) were also largely driven by the virus.

Scientists haven’t managed to completely sequence the virus in all affected species. Research and continuous surveillance could tell us how adaptable it ultimately becomes, and whether it can jump to even more species. We know it can already infect humans – one or more genetic mutations may make it more infectious.

At the crossroads

Between January 1 2003 and December 21 2023, 882 cases of human infection with the H5N1 virus were reported from 23 countries, of which 461 (52%) were fatal.

Of these fatal cases, more than half were in Vietnam, China, Cambodia and Laos. Poultry-to-human infections were first recorded in Cambodia in December 2003. Intermittent cases were reported until 2014, followed by a gap until 2023, yielding 41 deaths from 64 cases. The subtype of H5N1 virus responsible has been detected in poultry in Cambodia since 2014. In the early 2000s, the H5N1 virus circulating had a high human mortality rate, so it is worrying that we are now starting to see people dying after contact with poultry again.

It’s not just H5 subtypes of bird flu that concern humans. The H10N1 virus was originally isolated from wild birds in South Korea, but has also been reported in samples from China and Mongolia.

Recent research found that these particular virus subtypes may be able to jump to humans after they were found to be pathogenic in laboratory mice and ferrets. The first person who was confirmed to be infected with H10N5 died in China on January 27 2024, but this patient was also suffering from seasonal flu (H3N2). They had been exposed to live poultry which also tested positive for H10N5.

Species already threatened with extinction are among those which have died due to bird flu in the past three years. The first deaths from the virus in mainland Antarctica have just been confirmed in skuas, highlighting a looming threat to penguin colonies whose eggs and chicks skuas prey on. Humboldt penguins have already been killed by the virus in Chile.

A colony of king penguins.
Remote penguin colonies are already threatened by climate change. AndreAnita/Shutterstock

How can we stem this tsunami of H5N1 and other avian influenzas? Completely overhaul poultry production on a global scale. Make farms self-sufficient in rearing eggs and chicks instead of exporting them internationally. The trend towards megafarms containing over a million birds must be stopped in its tracks.

To prevent the worst outcomes for this virus, we must revisit its primary source: the incubator of intensive poultry farms.

Diana Bell does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.

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A major cruise line is testing a monthly subscription service

The Cruise Scarlet Summer Season Pass was designed with remote workers in mind.

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While going on a cruise once meant disconnecting from the world when between ports because any WiFi available aboard was glitchy and expensive, advances in technology over the last decade have enabled millions to not only stay in touch with home but even work remotely.

With such remote workers and digital nomads in mind, Virgin Voyages has designed a monthly pass that gives those who want to work from the seas a WFH setup on its Scarlet Lady ship — while the latter acronym usually means "work from home," the cruise line is advertising as "work from the helm.”

Related: Royal Caribbean shares a warning with passengers

"Inspired by Richard Branson's belief and track record that brilliant work is best paired with a hearty dose of fun, we're welcoming Sailors on board Scarlet Lady for a full month to help them achieve that perfect work-life balance," Virgin Voyages said in announcing its new promotion. "Take a vacation away from your monotonous work-from-home set up (sorry, but…not sorry) and start taking calls from your private balcony overlooking the Mediterranean sea."

A man looks through his phone while sitting in a hot tub on a cruise ship.

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This is how much it'll cost you to work from a cruise ship for a month

While the single most important feature for successful work at sea — WiFi — is already available for free on Virgin cruises, the new Scarlet Summer Season Pass includes a faster connection, a $10 daily coffee credit, access to a private rooftop, and other member-only areas as well as wash and fold laundry service that Virgin advertises as a perk that will allow one to concentrate on work

More Travel:

The pass starts at $9,990 for a two-guest cabin and is available for four monthlong cruises departing in June, July, August, and September — each departs from ports such as Barcelona, Marseille, and Palma de Mallorca and spends four weeks touring around the Mediterranean.

Longer cruises are becoming more common, here's why

The new pass is essentially a version of an upgraded cruise package with additional perks but is specifically tailored to those who plan on working from the ship as an opportunity to market to them.

"Stay connected to your work with the fastest at-sea internet in the biz when you want and log-off to let the exquisite landscape of the Mediterranean inspire you when you need," reads the promotional material for the pass.

Amid the rise of remote work post-pandemic, cruise lines have been seeing growing interest in longer journeys in which many of the passengers not just vacation in the traditional sense but work from a mobile office.

In 2023, Turkish cruise line operator Miray even started selling cabins on a three-year tour around the world but the endeavor hit the rocks after one of the engineers declared the MV Gemini ship the company planned to use for the journey "unseaworthy" and the cruise ship line dealt with a PR scandal that ultimately sank the project before it could take off.

While three years at sea would have set a record as the longest cruise journey on the market, companies such as Royal Caribbean  (RCL) (both with its namesake brand and its Celebrity Cruises line) have been offering increasingly long cruises that serve as many people’s temporary homes and cross through multiple continents.

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As the pandemic turns four, here’s what we need to do for a healthier future

On the fourth anniversary of the pandemic, a public health researcher offers four principles for a healthier future.

John Gomez/Shutterstock

Anniversaries are usually festive occasions, marked by celebration and joy. But there’ll be no popping of corks for this one.

March 11 2024 marks four years since the World Health Organization (WHO) declared COVID-19 a pandemic.

Although no longer officially a public health emergency of international concern, the pandemic is still with us, and the virus is still causing serious harm.

Here are three priorities – three Cs – for a healthier future.

Clear guidance

Over the past four years, one of the biggest challenges people faced when trying to follow COVID rules was understanding them.

From a behavioural science perspective, one of the major themes of the last four years has been whether guidance was clear enough or whether people were receiving too many different and confusing messages – something colleagues and I called “alert fatigue”.

With colleagues, I conducted an evidence review of communication during COVID and found that the lack of clarity, as well as a lack of trust in those setting rules, were key barriers to adherence to measures like social distancing.

In future, whether it’s another COVID wave, or another virus or public health emergency, clear communication by trustworthy messengers is going to be key.

Combat complacency

As Maria van Kerkove, COVID technical lead for WHO, puts it there is no acceptable level of death from COVID. COVID complacency is setting in as we have moved out of the emergency phase of the pandemic. But is still much work to be done.

First, we still need to understand this virus better. Four years is not a long time to understand the longer-term effects of COVID. For example, evidence on how the virus affects the brain and cognitive functioning is in its infancy.

The extent, severity and possible treatment of long COVID is another priority that must not be forgotten – not least because it is still causing a lot of long-term sickness and absence.

Culture change

During the pandemic’s first few years, there was a question over how many of our new habits, from elbow bumping (remember that?) to remote working, were here to stay.

Turns out old habits die hard – and in most cases that’s not a bad thing – after all handshaking and hugging can be good for our health.

But there is some pandemic behaviour we could have kept, under certain conditions. I’m pretty sure most people don’t wear masks when they have respiratory symptoms, even though some health authorities, such as the NHS, recommend it.

Masks could still be thought of like umbrellas: we keep one handy for when we need it, for example, when visiting vulnerable people, especially during times when there’s a spike in COVID.

If masks hadn’t been so politicised as a symbol of conformity and oppression so early in the pandemic, then we might arguably have seen people in more countries adopting the behaviour in parts of east Asia, where people continue to wear masks or face coverings when they are sick to avoid spreading it to others.

Although the pandemic led to the growth of remote or hybrid working, presenteeism – going to work when sick – is still a major issue.

Encouraging parents to send children to school when they are unwell is unlikely to help public health, or attendance for that matter. For instance, although one child might recover quickly from a given virus, other children who might catch it from them might be ill for days.

Similarly, a culture of presenteeism that pressures workers to come in when ill is likely to backfire later on, helping infectious disease spread in workplaces.

At the most fundamental level, we need to do more to create a culture of equality. Some groups, especially the most economically deprived, fared much worse than others during the pandemic. Health inequalities have widened as a result. With ongoing pandemic impacts, for example, long COVID rates, also disproportionately affecting those from disadvantaged groups, health inequalities are likely to persist without significant action to address them.

Vaccine inequity is still a problem globally. At a national level, in some wealthier countries like the UK, those from more deprived backgrounds are going to be less able to afford private vaccines.

We may be out of the emergency phase of COVID, but the pandemic is not yet over. As we reflect on the past four years, working to provide clearer public health communication, avoiding COVID complacency and reducing health inequalities are all things that can help prepare for any future waves or, indeed, pandemics.

Simon Nicholas Williams has received funding from Senedd Cymru, Public Health Wales and the Wales Covid Evidence Centre for research on COVID-19, and has consulted for the World Health Organization. However, this article reflects the views of the author only, in his academic capacity at Swansea University, and no funding or organizational bodies were involved in the writing or content of this article.

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