Missouri Department of Health Uses GIS to Track COVID-19 Viral Load in Wastewater

Methods of tracking Covid-19 are becoming more specific and exact as time goes on. With concerns of the spread of the COVID- 19 and its variants as well as the lack of comprehensive testing programs, many locations are turning to wastewater testing to effectively track the “viral load” of COVID-19 in their communities and help guide the battle against the spread of COVID-19. In the state of Missouri, officials are using GIS and mapping to track all the data around the spread of COVID-19 and guide policy and planning decisions.

In the state of Missouri, officials are using GIS and mapping to track all the data around the spread of COVID-19 and guide policy and planning decisions.

Jeff Wenzel, Bureau Chief of the Bureau of Environmental Epidemiology of the Missouri Department of Health and Senior Services, discussed the science behind this testing and how it is being used by policy makers and healthcare officials in Missouri, along wth Jeff Patridge, GIS Specialist for the State of Missouri, who discussed the dashboards, GIS and mapping tech that is being used in Missouri’s Sewershed Surveillance Project from the Missouri Department of Health & Senior Services.

Missouri Increasing Trends Pop Up

Missouri Decreasing Trends Pop Up

The Missouri wastewater testing program, called “The Sewershed Surveillance Program” is a collaborative effort from the Missouri Department of Health and Senior Services (DHSS), Missouri Department of Natural Resources and the University of Missouri.

“We started collecting data in April 2020,” said Wenzel.

“We found the signal for COVID-19 and were seeing increases in the viral load 4-6 days before seeing it in human cases,” said Wenzel. “The increased research became a more precise predictor that there would be 25% more cases with 70% more probability.”

In 2021 they were wondering if they could see the variants of concern. They began to see high frequency of mutations of interest as they entered the community. “We created StoryMaps to show trends over time, then added areas of concern to it.”

The community receives data from the StoryMaps almost as soon as the researchers themselves do. “We can reach out immediately if there’s a spike,” Wenzel said. “We have seen decreasing trends for a couple of weeks now.”

Missouri Trends Pop Up

Missouri has one of the most comprehensive wastewater testing programs in the nation with wastewater operators around the state voluntarily submitting weekly samples from more than 100 testing sites – effectively providing a weekly COVID-19 test to more than 50 percent of the state’s population. Combined with an advanced testing program that looks at key segments of the RNA sequence of COVID-19 and the use of GIS and mapping technology from Esri, Missouri is able to map the entire state showing COVID trends in cases and early identification of variants and their spread throughout the state. This type of visibility and tracking enables officials to predict areas where COVID-19 variants are spreading so they can allocate resources and services.

Weekly samples are collected from wastewater treatment plants and other access points such as manholes. The samples are filtered in the lab. Scientists extract and analyze the viral genetic material from the samples.

Two genetic markers called N1 and N2 are used to measure the viral load.

This PCR test is similar to the test performed on nasal swabs for diagnosis of COVID-19. However, where the nasal swab test detects whether the virus is present or not, this PCR test measures the viral load in the samples.

The viral load results are calculated.

The average of the N1 and N2 measurements is expressed as the number of viral marker copies per liter of wastewater.

This number is then combined with the flow rates for each facility to determine the number of viral marker copies per day.

The exponentially weighted moving average (EWMA) of the number of viral marker copies per day is used to identify trends in the data. Because these numbers are so large, they are expressed in multiples of 1 million.

Public health officials work with scientists to monitor trends in the data and inform communities.

Viruses constantly change through genetic mutation. As the COVID-19 pandemic has progressed, several variants of the COVID-19 virus (SARS-CoV-2) have emerged. Some variants may have a selective advantage due to their specific mutations, which might explain why some variants can become dominant over the “parent” strain (original strain of the virus).

In February 2021, the sewershed surveillance team began conducting variant testing of sewershed samples. Samples with sufficient SARS-CoV-2 genetic material are tested and analyzed for combinations of genetic mutations found in variants. “Because we are not analyzing entire genetic sequences, our results do not confirm the presence of a variant. However, they are suggestive of the presence and distribution of variants across the state and can help target follow-up in the communities.” – Missouri COVID-19 Sewershed Surveillance StoryMap.

Presumed Variant: detection of multiple markers unique to a single lineage.

Probable Variant: detection of a single marker predominantly from a particular lineage or lineages.

Results Unavailable: Often due to viral particle concentrations in the sewershed being too low to conduct this type of testing.

“We’re looking at new variant of concern as the virus is decreasing, among the new cases,” said Wenzel. “In those areas we increase testing and availability of vaccine.”

As the virus moved from Delta to Omicron, they developed different treatment strategies. “We knew when Omicron was becoming dominant in the wastewater,” said Patridge. “If it’s in the wastewater, we’re looking at all the mutations, RNA that can bind to our cells differently and evade treatments.”

There are different characteristics of the variants, said Wenzel. Both Alpha and Omicron appeared first in big cities and moved south from St. Louis, then got into rural Missouri. With Delta the rural communities contracted it first. “Omicron was associated with travelers, so large cities and interstate movements spread it. Missouri got Delta earlier than other states, and Omicron was later.”

Lab samples

Many states, the UK and the Netherlands are using wastewater tracking of COVID-19 now. The CDC has begun to collect samples throughout the U.S.

The variant of concern can also shed the viral load differently. “Our samples are collected prior to wastewater treatment processes, so there are many pathogens present before they are filtered out by the chemical wastewater process and released into the environment,” said Wenzel. “The COVID-19 being tested doesn’t get into drinking water and plants.”

There are different methods of collecting data. “The information is good, it depends on what questions you ask,” said Patridge. “We’re looking at receptive binding domain where you can put all sections in order. Many others look at the entire RNA strand that are difficult to piece together with a lot of data to process. We process 1 TB of data per receptor bind domain RBD.”

Patridge said they have improved predictions. “One way to do that is to look at locations where the process doesn’t work, i.e., there is too much or not enough viral load, and the number of people in a community or at an event, getting a measurement of the population at a work place.”

Here is a link to Missouri’s state-wide COVID-19 wastewater testing program, including maps showing rates in every region of the state as well as how the data is trending: Missouri State Wide COVID-19 Wastewater Testing Program

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