Throat Swab? Nose? Best Test Yet of Omicron’s Spread May be a Sewage Sample
“Swabbing” a sewage bore near the beach in Israel for SARS-CoV2 – could sewage be the best indicator yet of the spread of Omicron and other viruses?

Two years into the COVID-19 pandemic, monitoring sewage for evidence of disease – in this case COVID-19 – may be on the verge of becoming mainstream. 

At least that is what some trend-setting researchers are hoping, hoping to detect rising SARS-CoV2 infections early and set policies based on data even before swab testing can provide it. 

The virus spreads from person-to-person via droplets expelled from the mouth and nose. But it is also shed by infected people every time they go to the bathroom – though there is no evidence to date that anyone has become sick with COVID-19 because of direct exposure to treated or untreated wastewater, according to the United States Centers for Disease Control and Prevention (CDC). 

Wastewater epidemiology – turns human waste into a ‘data asset’

In fact, tracking the evolution of new pathogens through sewage is not a new tactic. It’s been used by researchers to probe the expansion of antibiotic resistant bacteria in  Africa and South-east Asia as well as by some national health ministries for more routine surveillance of relatively rare but deadly diseases like polio.

But the overwhelming pace of Omicron’s spread- which has made it impossible for health experts to keep up usually the traditional, individually-based testing and surveillance tactics – could help transform such approaches into more of a trend.

Along with high income countries like the United States, Canada and Israel, South Africa is on the cutting edge of such surveillance, while pilot projects are underway in several countries of Latin America.  And now, a loose network of researchers and universities, called the COVID-19 WBE Collaborative have taken the idea to the next level – creating a global map of wastewater-based COVID monitoring sites in some 58 countries worldwide.  The is funded by the University of California at Berkeley’s CITRIS and Banatao Institute’s tech innovation hubs.

“Wastewater epidemiology turns human waste into a data asset that can improve the health and safety of populations,” explained Casey McGinley, chief of staff of Massachusetts-based Biobot Analytics, which also is conducting tests in Mexico, and piloting new surveillance projects with the World Bank in Uruguay and Ecuador.

“Wastewater analysis data is a great complementary tool to traditional public health surveillance methods that rely on clinical testing. Results can be used for different purposes and have a unique role to play at each stage of the pandemic, from early detection to detection of resurgence.”

Undercounting of Omicron cases makes wastewater-based surveillance more relevant

Ari Goldfarb, founder and director general of Kando

McGinley told Health Policy Watch that wastewater-based disease surveillance has become increasingly relevant since the start of the Omicron wave, partially because “due to incredibly high demand, availability of testing is very limited and there are long delays in reporting clinical testing results” and because “many individuals are expecting mild symptoms and resorting to at home tests which are not reported in official statistics.

“Against this backdrop of undercounting cases, wastewater data is a very important data set that gives a comprehensive overview of the magnitude of infections,” she said.

In Israel, Kando, a company that uses AI and Big Data to sample and analyzes wastewater to improve management in sites around the world, just launched a partnership with the Health Ministry and several leading universities to apply its technology in hundreds of communities across the country to monitor for Omicron and any future SARS-CoV2 variants. 

According to the plan, towns of more than 20,000 people will be monitored twice a week using a series of sensors and control units placed in municipal sewage systems.  The samples collected will be sent to laboratories at Ben-Gurion University where PCR tests suitable for wastewater are conducted. In the event that the results received are positive, an additional test is carried out to quantify the Omicron variant and other variants. Sample results will be feed into a national computer data base that can analyze the results based on big data models and AI.

The entire process takes about 24 hours – from sample to results – but in this case for an entire neigborhood or town – rather than just one individual.

“You can look at wastewater as gigabytes of data running just under the city,” Kando CEO Ari Goldfarb told Health Policy Watch.

An important complementary tool – particularly in light of the increased reliance on rapid tests

Wastewater testing has become even more immediately relevant for tracking COVID, as countries pivot to greater reliance on rapid antigen tests, while gold-standard PCR tests are reserved for older people, those at higher-risk or with more serious symptoms. With people using less accurate at-home tests, which they also often fail to report, sewage surveillance could fill valuable missing holes of data.  

Better data on the relative proportions of Omicron versus other variants is another benefit of such initiatives, explained McGinley of Biobot. 

Her company reports the concentration of all SARS-CoV-2 variants detected in wastewater samples, including Omicron. In addition, Biobot is doing R&D work to detect and measure the percentage of the Omicron variant in wastewater through genomic sequencing. That can help decision-makers know how dominant Omicron has become, in relation to its more deadly but less contagious cousin, the Delta variant. 

“This information helps decision-makers in the current COVID-19 surge to understand the scale of infections, since case data has become significantly less reliable, tailor public health messaging around mask wearing and indoor gatherings, and lastly plan hospital resources accordingly,” McGinley said. 

In the US model, Biobot is sending internally devised wastewater sampling kits to public sector and corporate customers – containing everything needed to collect, package and safely ship the wastewater back to the company’s lab in Cambridge. Once received,  the company screens the samples to identify the presence and amount of the virus in each sample. The results are processed through Biobot’s data pipeline and reports are generated and sent back to the customers. 

Biobot’s open source sewage surveillance in the United States.  Surveillance curve parallels clinical case reports – but with higher absolute levels of disease incidence.

Its customers have included sites in all 50 states, as well as Canada and Mexico. Currently, Biobot’s National Monitoring Network reports data from approximately 200 communities in more than 20 US states. 

Through a partnership with the World Bank, Biobot has also worked on capacity building for wastewater monitoring for COVID-19 in Ecuador and Uruguay. 

US CDC – Stepping up COVID Wastewater Surveillance

CDC, however is now stepping into the scene with it own COVID wastewater surveillance program, which aims to provide a systematic, national network of pathogen-hunting sites, as well as guidance to communities about how to undertake sampling, said Brian Katzowitz, a health communications specialist from the CDC’s Division of Foodborne, Waterborne and Environmental Diseases.

“CDC just began funding a commercial wastewater testing contract which will provide twice weekly SARS-CoV-2 wastewater testing to 500 sites nationwide,” Katzowitz told Health Policy Watch. “With the emergence of Omicron, we were able to include Omicron tracking specifically into the contract. In addition, we are updating our data system to be able to receive, analyze and report Omicron-specific data to health department partners.”

He cautions, however, that “variant detection with wastewater is a little bit tricky” and as a result, “variant tracking data has to be interpreted carefully” – using sophisticated modeling techniques

“Sequencing samples from wastewater cannot confirm the presence of a specific variant because SARS-CoV-2 RNA decays quickly in wastewater,” he explains.  “Instead, variant-specific wastewater sampling looks for specific mutations, and the methods used cannot detect if all of the variant-defining mutations are present on a single genome.”

South Africa, Latin America, Canada and others joining the wastewater Omicron search

Multiple other countries are also using sewage surveillance to help crack Omicron- as evidenced by the proliferation of new projects on the COVID19WBEC.org dashboard.  

Researchers in South Africa, where virus hunters in Tshwane (Pretoria), were able to detect how the Omicron wave there, where it was first identified, was reaching a peak equal to that of the earlier Delta variant in late November – only days after the variant had first been announced and named by WHO.

Similar programmes have been reported by public health departments in Australia, Canada – and beyond.  

In Ottawa, Canada, wastewater collected by the Robert O. Pickard Environmental Center is being measured for coronavirus genetic material.

 “In essence, we are conducting a very broad COVID-19 survey to which we all contribute including those who are not getting tested themselves and those who may not even know they are infected,” Ottawa Public Health’s website explained. It added that wastewater is collected and transported to a laboratory five days per week where viral RNA levels are immediately tested, and results reported the next morning.

“It is very exciting that we can do these things to improve public health,” Goldfarb said. 

Image Credits: Kando , Biobot .

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