The Covid-19 virus can be picked up in wastewater before it’s found in a clinical setting and researchers in a new study say this could be really useful for tracking new mutations of the virus, like the B.1.17 strain that is now widespread in the U.K. and has already been introduced in the U.S.

“SARS CoV-2 virus is excreted by individuals that are infected by Covid -19 and the fecal waste ends up in the wastewater systems. By sampling wastewater, we can get information on infections for a whole population. Some wastewater systems serve several thousand people. Some serve hundreds of thousands of people,” explained the study’s lead author Kara Nelson, from College of Engineering at the University of California-Berkeley.

“Sampling wastewater is a very efficient way to get information. It is also a less biased source of information, because we can get information from all individuals in the sewershed, whether or not they are being tested in a clinic. We know that there are individuals that have asymptomatic infections that may never get tested.” 

The study was conducted using sewage from the San Francisco Bay area and they found when they analyzed the wastewater that the SARS-CoV-2 genomes that was detected in the sewage was the same as the genomes found in the clinics of the same region.

Additionally, the researchers also detected variants of Covid-19 that had only been reported from elsewhere in the United States or globally, which means they were able to find new strains before they were found by local clinics.

Nelson explained that by understanding which strains of the virus are present in populations over time, researchers can gain insight into how transmission is occurring and whether new variants, like B.1.1.7, are dominating transmission. 

“Of everyone who gets tested, only a fraction of those samples even get sequenced. When you are sampling the wastewater, you get a more comprehensive and less biased data on your population,” she said.

“It appears that we might be able to get an earlier signal in the wastewater if a new variant shows up compared to only relying on the sequencing of clinical samples. Just knowing that SARS-CoV-2 is present in a population is the first step in providing information to help control the spread of the virus, but knowing which variants are present provides additional but very useful information.”

This adds to earlier research which has shown just how crucial waterwaste epidemiology can be at preventing outbreaks.

In August, the University of Arizona’s sophisticated surveillance system caught asymptomatic cases early.

Further, a Yale University study published in Nature Biotechnology that measured SARS-CoV-2 RNA concentrations in primary sewage sludge in the New Haven metro area found their results led hospitalizations by one to four days and positive test results by approximately one week.

So it’s no surprise many countries are already starting to utilize this method to get a better handle on the Covid-19 virus spread.

For example, in France Marine Firefighters in Marseille have used water samples taken from drains to map the spread of the Covid-19 virus in the city, and prevent clusters forming in elderly care homes.

They’ve also done similar things in the U.K. , Italy, Australia, and Canada to get ahead of the virus spread.

In mid-August, the Centers for Disease Control and Prevention (CDC) and the US Department of Health and Human Services (HHS) announced they were initiating a National Wastewater Surveillance System (NWSS) in response to the COVID-19 pandemic.

And by late September that HHS said they were expanding national efforts. According to CNBC, they posted a notice saying they were “seeking bids from contractors that can carry out a plan to test up to 30% of the country’s wastewater to act as an ‘early warning system’ for coronavirus outbreaks.” 

However, despite mounting evidence on it’s efficacy there hasn’t been much progress on rolling out a nationwide surveillance system. According to the latest from the CDC they’re still “developing a portal for state, tribal, local, and territorial health departments to submit wastewater testing data into a national database for use in summarizing and interpreting data for public health action.”

And the slow progress might be in part due to the fact that monitoring sewage for traces of the pathogen is a challenge.

In order to find the virus in the soup of bacteria and other genomic material, researchers need to separate and isolating the virus fragments from the wastewater – a task often easier said than done as there may be many different strains present due to the number of people contributing to the sample.

In this latest study, published in mBio, an open-access journal of the American Society for Microbiology, not only found they could use wastewater to track Covid-19 but the researchers developed and used a new method for sampling wastewater.

“One contribution of this paper is the ability to prepare samples for sequencing from wastewater. Instead of directly sequencing everything present, we used an enrichment approach where you first try to enrich the RNA that you are interested in,” explained Nelson. “Then we developed a novel bioinformatic analysis approach which was sensitive enough to detect a single nucleotide difference. You can’t get any more sensitive than that.” 

In other words, the researchers made the Covid-19 genetic signal louder and they also made the computer that looks for that signal more sensitive to that signal. It’s kinda like if turned up the volume on the stereo and put in hearing aids.

But before a nation-wide sewage surveillance is rolled out there’s more work to be done.

As Katherine Ellen Foley writes in Quartz: “Getting there will require major investment, though. Sewers weren’t built to be monitoring systems. Not all public health departments have a large enough staff to take on extra roles, or nearby labs to analyze samples. And even those that do have the right resources have no idea what to look for: There’s no standardized way to measure the components of wastewater, which for now makes it impossible to compare data from region to region.”

So if we can surmount those hurdles we might stand a chance of finally get this virus under control.

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