UP scientists propose wastewater-based epidemiology for Covid-19 surveillance

IN THE WATERS. A group of scientists from the University of the Philippines are recommending the use of Wastewater-Based Epidemiology in detecting Covid-19 in communities. The scientists found that based on samples collected from some areas along the Davao River that "in some cases, Sars-Cov-2 RNA was detected in community wastewaters in Davao City even when no new cases of Covid-19 were reported for the corresponding week." PHOTO BY MARK PERANDOS
IN THE WATERS. A group of scientists from the University of the Philippines are recommending the use of Wastewater-Based Epidemiology in detecting Covid-19 in communities. The scientists found that based on samples collected from some areas along the Davao River that "in some cases, Sars-Cov-2 RNA was detected in community wastewaters in Davao City even when no new cases of Covid-19 were reported for the corresponding week." PHOTO BY MARK PERANDOS

IT seemed long ago but it can be "mindblowing" that the Covid-19 pandemic struck roughly around three years ago.

March 2020. A month everyone will remember as our government implemented a hard lockdown in a bid to manage the spread of Covid-19 considering that we were still in uncharted waters then.

But as the days went on, modern science has allowed the development of new treatments, health responses, and surveillance methods. Vaccines and medicines were developed and people now have the basic knowledge of how to deal with Covid-19.

When it came to surveillance, one of the effective ways was mass testing, which can be costly. Despite not having the resources of major economies, Davao City focused on targeted testing to be able to identify and treat individuals with Covid-19.

However, Dr. Dann Marie del Mundo, the project leader of the DOST-Nicer iWas Project and the Department Chair of the Department of Food and Chemistry of the University of the Philippines-Mindanao (UP-Min), said the Philippines' heavy reliance on RT-PCR-based clinical diagnostics of symptomatic individuals and their contacts poses several challenges.

"It has limitations in the early detection or prediction of community outbreaks, it is logistically demanding and also it is expensive so there must be another tool for Covid-19 surveillance, Del Mundo said.

A group of scientists from UP has recently published a study on the use of Wastewater-Based Epidemiology (WBE) as a surveillance tool for Sars-CoV-2, the coronavirus causing the Covid-19.

"It uses chemical or biological markers that are sourced from waste-waters, pooled wastewaters, that provide us information on the overall health of the community. So this can be a supplementary or complementary data set for public health surveillance," Dr. Caroline Marie Jaraula, Project Leader of the USAid Peer Peoples Project and an Assistant Professor at the UP Marine Science Institute, said during the presentation of their study in January 2023.

Wastewater-Based Epidemiology

Jaraula said they were already conducting a water quality study in parts of Davao River under USAid's People's Project, which stands for Baselining Persistent and Emerging Organic Pollutant Levels in Environmental and Engineered Systems for Healthy Philippines.

Based on the study, they were able to gather different data to look into the quality of the waters of Davao River. Among the data they gathered were the E. Coli and Coliform levels in the river.

"From these two data sets [we] we're able to identify which parts of the Davao River have untreated wastewater and that could be useful for initial surveys on wastewater-based epidemiology since we don't have sewers that are connected to wastewater treatment plants," Jaraula said.

Jaraula and her team will eventually expand this study to see if they can use a similar method to detect Sars-CoV-2.

In March 2020, they attended a webinar organized by the Philippine American Academy of Sciences and Engineers where Dr. Francis Delos Reyes was a speaker.

"That webinar was about the use of wastewater-based epidemiology for Sars-CoV-2 or Covid-19 very early on in the pandemic," Jaraula said.

Based on the presentation, Delos Reyes and his team detected Sars-CoV-2 in the wastewater and identified that community at risk.

"So, for a lot of people who are asymptomatic and do not need to go to the hospital, they did not know they have that Covid-19 so we lost that data from clinical reports of positive Covid-19," Jaraula said.

She said that based on what they have seen from Delos Reyes' presentation, the waste-water pooled sample "is very effective in showing which groups of the community would have that kind of disease."

"This has very high potential waste water-based epidemiology to serve as one of the forecasting tools to identify communities at risk or might be at risk," Jaraula said.

Del Mundo said Covid-19 paved way for WBE with over 70 countries using it in their Covid-19 surveillance.

"Studies have shown that Sars-CoV RNA is shed in the feces of symptomatic and asymptomatic individuals with Covid-19. So, this WBE can be a complementary tool for Covid-19 surveillance since it is based on the premise that wastewater represents a snapshot of the status of the public health of a certain community," Del Mundo said.

Jaraula and Del Mundo, together with a team of scientists, submitted a proposal to UP-Min for the pilot investigation of Sars-Cov-2 Wastewater-Based Surveillance in Davao City. Scientists and researchers from UP Mindanao and UP Manila that are also part of the study are Dr. Lyre Anni Murao, Dr. Emmanuel Baja, Dr. Vladimer Kobayashi, and Maria Catherine Otero.

"The main objective of our pilot study is to employ waste-water-based epidemiology and whole-genome sequencing (WGS) as approaches for Covid-19 surveillance in low-resource and low-sanitation barangays in Davao City, Philippines," Del Mundo said.

The scientists coordinated with the Davao City Health Office and some barangays to identify creeks and sewer pipes as part of their sampling sites.

"We had six barangays initially, these areas have been classified that time by CHO as low-moderate to high risk of Covid-19 transmission," Mundo said. These barangays are 23-C, 76-A Bucana, Leon Garcia, Matina Crossing, Mintal, and Monteverde.

The sampling period for the study was conducted from November to December 2020.

"From the wastewater sample, we processed them and then we detect or we check the presence or absence of the virus. With a positive detection, we processed it again for Whole Genome Sequencing to check the mutations," Del Mundo said.

Their study showed that 22 out of the 24 or 91.7 percent of the samples obtained from the six communities over the four-week course of the study tested positive for Sars-CoV-2.

Promising results

Following their study, results have shown that the WBE can be an effective means to detect Covid-19 in communities.

"Sars-CoV RNA was detected even if [where] the wastewater [were from] were classified as having low risk of Covid-19 transmission and were reported to have no new cases," Del Mundo said.

The study also showed that "in some cases, Sars-Cov-2 RNA was detected in community wastewaters in Davao City even when no new cases of Covid-19 were reported for the corresponding week."

Del Mundo said this "suggests that Sars-CoV-2 RNA detected in community wastewater may come from pre-symptomatic, asymptomatic, or symptomatic individuals who did not self-report to their local monitoring unit."

Another important result whey found was after processing the wastewater samples that were detected to have Sars-CoV-2 RNA, they were able to detect mutations that were previously not reported.

"We found the existing mutations and we also detected mutations that were not yet reported at that time. This means that wastewater genomic surveillance can facilitate the early detection of mutations using fewer resources because we are using the wastewater which represents the pool of individuals for our study," Del Mundo said.

She said the detection of Sars-CoV-2 RNA in barangay wastewater in Davao City indicates that WBE and WGS can be practical complementary health surveillance tools for Covid-19.

"Detection of Sars-CoV-2 RNA in barangays with low risk of Covid-19 transmission signifies the potential of WBE for unbiased reporting of Covid-19 infections," Del Mundo said.

She said WBE can generate trends in community transmission of Covid-19, while WGS can identify mutations that may impact public health interventions.

Challenges

Del Mundo said Davao City's lack of a centralized wastewater treatment facility makes WBE challenging in not only Davao City but in the country too.

"Other countries which are using WBE as a COVID-19 surveillance tool, they have a wastewater treatment plant but that is lacking in the Philippines, specifically in Davao City, not all or some areas really have no wastewater management treatment system," Del Mundo said.

The researchers said centralized wastewater treatment plants (WWTPs) will provide scientists with the necessary data to provide a clearer picture of the situation.

"With WWTPs, accurate data about the population served by the specific treatment plant are available, and biological, physicochemical, and hydrologic data are regularly monitored, permitting near-real-time spatiotemporal trend analysis on Covid-19 transmission in the served population," the researchers said.

Another limiting factor for WBE in the Philippines and Davao City is "there is incomplete data on sewer pipe networks in the communities."

"Sewer pipe networks are very important in tracing the contributors of the virus," Del Mundo said.

The researchers add that "cities without centralized WWTP that plan to implement WBE, whether for Covid-19 or other water-related infectious diseases, must ensure that a comprehensive map of sewer networks is first generated to accurately identify the population contributing to the wastewater."

Post-pandemic

However, with the improving Covid-19 situation, is there still a need to conduct WBE as a form of surveillance?

Catherine Otero, Ph. D. candidate in Health Sciences at the University of the Philippines Manila, said while there are those who question the relevancy of the WBE post-pandemic, the system they established through the study will complement the efforts of the government in detecting other diseases.

"The system, the framework that we were able to develop can actually be adopted to other diseases like Antimicrobial Resistance (AMR), polio, measles, dengue, and for those diseases that are water-related," Otero said.

The scientists said the findings from the study "provide a baseline framework for the application of WBE in low-sanitation metropolitan areas such as Davao City, Philippines, even for other infectious diseases of public health relevance."

She said the WBE will complement the Department of Health's surveillance system for polio and other vaccine-preventable diseases.

"We recommend that a similar multifaceted assessment be conducted in other low-sanitation areas prior to WBE implementation," the researchers said.

Otero added that continued support for this effort will also support the goal of becoming a "more epidemic-resilient country or city." RJL

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