Tag: coronavirus

Mathematical tools to aid in the interpretation of coronavirus testing

New mathematical equations co-developed by Puget Sound Institute affiliate research professor Marc Mangel are designed to help health officials interpret coronavirus test results for better risk assessments. 
As more people in the U.S. are vaccinated and mask restrictions loosen, public health officials hope that the coronavirus pandemic has reached a turning point. Even so, the virus continues to rage around the world and concerns remain for people who are unvaccinated or may have compromised immune systems. Testing for new infections continues to be a critical tool in the fight against the virus.
One of the most common coronavirus tests is the rapid antigen test, which can be done without laboratory analysis in as few as 15 minutes. Its speed and convenience are a big plus when dealing with a quickly spreading virus, but the test is prone to errors, sometimes showing false negative or positive results, especially when it is conducted in the early stages of the disease. As a result, just based on testing, it is often difficult to know the true rate of infection in a community.
That’s a challenge for health officials and it can have big impacts on policy decisions. The number of coronavirus cases in a community can help determine when a county allows public gatherings. It can help hospitals assess the need for critical resources like respirators and medical staff. Now, a new mathematical tool developed by Puget Sound Institute affiliate research professor Marc Mangel in collaboration with Alan Brown of Johns Hopkins University is available to help health officials better gauge case rates, and to calculate the risk of exposure to the virus in groups of different sizes.
The method is outlined in a paper released by Johns Hopkins University and describes a series of equations “that can be implemented in a spreadsheet or using a handheld calculator,” Mangel and Brown write, making them accessible to non-mathematicians. Public officials can use the equations to correct for the testing errors and then advise policymakers on where to prioritize resources.
“Suppose a group of people go to a wedding and the next day learn that someone tested positive, so they all go out to get tested,” Mangel says. “Most tests are not as accurate early in the infection,” he says. “Our equation is a way of better interpreting the results of those tests — what the true risk is.”
While the equation itself does not give an exact case count, Mangel says, it allows officials to get closer to the true number of infections by providing reasonable upper and lower bounds for the estimate. The result can be visualized as a curve on a graph. Users can draw horizontal and vertical lines that intersect with the curve based on risk percentage and group size (see the graph labeled “Figure 2” from the paper), although the curve becomes less useful as case rates approach zero.

A figure and text from the paper ‘Operational analysis for coronavirus testing: Recommendations for practice’ published by Johns Hopkins University.

The equation involves math similar to that used in the fishery sciences, says Mangel, who specializes in mathematical biology and applies mathematics to Puget Sound recovery work. Mangel’s work often spans across disciplines, from cybersecurity to social networks, and now epidemiology. He compares the current equation to one used in juvenile rockfish surveys in the California Current. In that case, for example, there will be a certain number of false positives or negatives when counting fish, and scientists can use similar math to account for identification errors.
“One of the great things about mathematics is that it allows you to see commonalities in systems that on the surface look completely different,” says Mangel who hopes the same equation could be used in the event of other outbreaks of infectious diseases beyond Covid-19. “Next time, we would like to be more prepared.”

An endangered southern resident orca leaps out of the water in Puget Sound. Photo courtesy of NOAA.

Research in the time of the coronavirus

As the state’s stay-at-home order drags on, much of the work to recover Puget Sound has shifted online. Funding schedules for the state and federal Strategic Initiatives remain on track and events like the Salish Sea Ecosystem Conference are going virtual next week with presentations by video conference.
But researchers face an entirely different situation as labs are shuttered and field work is cancelled almost across the board.
Megan Dethier, director of the University of Washington’s Friday Harbor Laboratories calls the situation at her lab fairly typical. Friday Harbor, known for its hands-on research among the tide pools of San Juan Island, is in “maintenance mode” as scientists work out which projects are critical and which ones can go on hold for the near future.
“Right now, we’re mostly trying to keep things from dying or crumbling,” Dethier said. On any given day, she told PSI over the phone, one scientist ventures into the office to exercise the valves on her electron microscope. Others come in to feed the captive fishes, but few are doing active research. The field study classes that have made Friday Harbor famous as a place for experiential learning have been cancelled as university courses go online.
“You just can’t do that virtually,” Dethier explains. “A quarter abroad in Rome is not the same as watching a bunch of videos about Rome.”
Dethier hopes that more field research will proceed later in the spring or summer if restrictions lift, but for now, as for most scientists, it is a good time to write papers and crunch old data.
Jenna Judge, monitoring lead for the Puget Sound Partnership says members of the Puget Sound Ecosystem Monitoring Program have been meeting to discuss ways to continue studying Puget Sound environmental conditions while staying safe and complying with the state’s social distancing mandates.
With exceptions for research deemed critical to safety or conservation needs, Judge says, most scientists at state and federal agencies and universities are not allowed to go into the field to do their studies. “We’re assuming that most field research is shut down right now,” she says. That means huge amounts of monitoring data for the spring — from herring counts to water sampling — are expected to be lost. At the same time, scientists are hoping to study what the global decrease in human activity might reveal about human pressures on the ecosystem.
The report that impacts from the virus have, temporarily at least, reduced the global carbon footprint is one dramatic example. Carbon emissions dropped by 18 percent in China between February and mid-March during the height of that country’s coronavirus lockdown and regions all over the world are reporting cleaner air.
Amy Snover, director of the University of Washington’s Climate Impacts Group told KIRO News, “We are seeing reduced emissions for really horrible reasons,” but she hopes that society can use this as a wakeup call “that actions that I take today will affect the impacts on you tomorrow.”
Fewer cars on the road and airplanes in the sky have also meant less noise in the environment. Seismologists have even observed a drop in vibrations on the Earth’s crust. 
One remaining question is whether the coronavirus shutdown has influenced noise in the oceans. Vessel disturbance has been a big problem for Puget Sound’s endangered southern resident orcas because it has interfered with the whales’ ability to use echolocation to hunt for scarce salmon. Could ocean noise be declining as well?
One source on this is the Orcasound hydrophone network run by orca scientist Scott Veirs. While Veirs, too, is staying at home, “We have acoustic data that continues to come in as long as those hydrophones don’t break,” he says.
Veirs suggests that now is a great time to listen to the hydrophone network that streams live sounds 24 hours a day from beneath the waters of Puget Sound. The network listens for the sounds of marine mammals such as Puget Sound’s orcas and other whales, but also captures shipping noise.
While the number of large vessels crossing Puget Sound has not decreased much during the COVID-19 crisis — the current numbers actually exceed those from just five years ago, according to the Marine Exchange — anecdotal reports from around Puget Sound suggest the number of smaller vessels may have declined. “That’s what my ears tell me, anyway,” says Veirs, “although we haven’t analyzed the data.”
If indeed small vessel activity and related noise levels have decreased, Veirs wonders how this might affect the southern residents. The orcas are not currently known to be in Puget Sound, but if they arrive, Veirs hopes scientists will be ready to analyze their behavior in this brave new environment.
“If the southern residents come back, the whales are potentially going to be in a very different situation. My gut tells me it is almost surely a good thing for the southern residents to not have all those boats out there,” Veirs says. But will there be observers out on the water to record what happens? Scientists can only hope.

An illustration of the coronavirus. Image courtesy of the Centers for Disease Control and Prevention.

The coronavirus has been found in Tacoma sewage. It could help scientists track the pandemic

Researchers at a non-profit biotech startup in Tacoma have found traces of the novel coronavirus in the city’s sewage, opening up new possibilities for tracking and monitoring the COVID-19 pandemic. The testing is being led by Center for Urban Waters collaborator David Hirschberg who directs the RAIN biotech incubator in Tacoma, along with RAIN’s principal scientist Stanley Langevin and recent University of Washington Tacoma graduate Ryan Culbert who ran the tests.
“We found it,” said Hirschberg, who began collecting samples of raw sewage and sludge from the city’s Central Wastewater Treatment Plant in recent weeks. “The [coronavirus] is in there. There is no way it can’t be.” Hirschberg said the levels of the virus were very low and “we don’t think it is infectious,” but the presence of the virus may help scientists in the battle to identify infection hot spots around the world. The evidence was found in raw sewage influent referred to as “water sludge” by wastewater treatment officials.
Stuart Magoon, the assistant division manager of Environmental Services for the City of Tacoma said he had been informed by Hirschberg that the virus had been found in Tacoma sludge, but that its presence did not pose any additional threat to workers who were already taking standard precautions. “There are plenty of things in sewage that you don’t want to get exposed to,” he said, “so the technicians are already very careful.” In addition, experts believe the coronavirus was found at such tiny amounts that it was not in an active or virulent form.
Hirschberg, who specializes in environmental monitoring for diseases is an independent researcher who has worked for many organizations, including the U.S. Department of Defense, to develop monitoring systems for dangerous pathogens such as anthrax. His group received permission from the City of Tacoma to test sewage in the hope of developing a “tripwire” for tracking the outbreak.
“We really believe this could be an early warning system,” Hirschberg says. Currently, most testing, where it is available, focuses on individuals, but Hirschberg says the ability to find coronavirus in the environment would allow health officials to focus their testing or identify when new outbreaks occurred. That could be especially helpful for catching many cases where people may have no symptoms, or in the early stages of the infection before patients are identified. There are currently more than 330 confirmed cases of the coronavirus in Tacoma and more than 10,200 in the state of Washington.
Hirschberg could imagine setting up inexpensive tests in different communities where health officials could mobilize to protect local schools or start more aggressive testing in certain areas. Other scientists around the world are looking for similar ways to test for the coronavirus in the environment. An article in the April 3rd issue of Nature described how wastewater could be used as an “early warning sign if the virus returns.” Countries such as the Netherlands are already planning to step up wastewater monitoring for the novel coronavirus, the article says.
In addition to sewage, Hirschberg’s group at RAIN is hoping to detect the coronavirus on surfaces and in the air. His group has developed similar tests for dangerous pathogens, such as anthrax and other, earlier forms of SARS. “We have the tests and we have the technology,” Hirschberg says. However, government regulations for clinical laboratories have limited the ability of small labs such as RAIN to conduct testing. The expenses of following the government’s CLIA (Clinical Laboratory improvement Amendments) guidelines, for example, have been prohibitive. “It is absolutely slowing our response,” he says. Since the coronavirus pandemic hit, Hirschberg has been working with CLIA-certified labs to share ideas and improve the efficiency of testing and monitoring. “People are dying every day,” he says. “This kind of testing takes time and money, but we can’t afford to wait. We just need to start saving lives.”
Other long-term surveillance by Hirschberg’s group could include analyzing bat guano in the region to see if the virus or a version of it has migrated back into its original host organism. Epidemiologists believe coronavirus originated in bats in China.
Hirschberg says his approach to finding pathogens in the environment is similar to how scientists at the Center for Urban Waters and other groups use cutting edge analytical instrumentation and innovative data mining tools to look for markers of human activity, such as toxic chemicals in Puget Sound. Few scientists monitor for pathogens, he says, but that may be changing as the coronavirus raises public awareness of the impacts of disease. Hirschberg sees environmental testing as a critical tool for monitoring all sorts of outbreaks, including those in wildlife. “We should be very careful when things are dying around us,” Hirschberg says, whether it is salmon or orcas in Puget Sound, or humans facing a pandemic.