Estimating COVID-19 spread by looking at past trends of influenza-like illnesses

June 26, 2020

Science Daily/Montana State University

In order to better understand the spread of the novel coronavirus, new research examines trends in visits to outpatient clinics for influenza-like illnesses in March 2020 as compared to previous years.

How many people in the U.S. have had COVID-19? Using a database of information collected after the 2009 H1N1 outbreak, a Montana State University researcher is helping develop a better understanding of the spread of the novel coronavirus.

Alex Washburne, a researcher in the Bozeman Disease Ecology Lab, which is housed in the College of Agriculture's Department of Microbiology and Immunology, published a paper on the subject this week in the journal Science Translational Medicine. The paper uses data from ILINet a database created by the Centers for Disease Control and Prevention in 2010 to count patients who check into medical clinics with influenza-like illnesses, or ILI. That type of data collection for the purpose of identifying trends is known as syndromic surveillance.

Influenza-like illnesses include any number of infections that carry symptoms similar to the seasonal flu -- such as fever, cough and sore throat. Both influenza-like H1N1 and non-influenza diseases like COVID-19 fall into that group. Monitoring trends in ILI clinic visits, Washburne said, could help better understand how quickly and extensively COVID-19 spread during the early days of its appearance in the U.S.

In collaboration with researchers at Pennsylvania State and Cornell universities, Washburne examined the number of ILI visits reported each week over the last decade and compared those historical trends to such visits during March 2020. They identified a surge in March 2020 ILI visits that parallels regional increases in COVID-19 cases.

By examining ILI data alongside the known regional prevalence of COVID-19, Washburne and his collaborators determined that there may have been many cases of the coronavirus disease that weren't initially identified as such.

Washburne and his colleagues estimate that as many as 87% of coronavirus cases were not diagnosed during early March, which could translate to around 8.7 million people based on the excess March ILI visits. The surge in ILI diminished quickly in the latter part of March, leading researchers to conclude that more cases of COVID-19 were being identified since fewer ILI reports were being logged in the database.

"Early on there seems to have been a low case detection rate, but as time went on that changed," said Washburne. "By the last week in March, as more and more testing was going on, that case detection rate increased significantly."

This is good news for scientists seeking to predict and prepare for future epidemics, said Washburne. A baseline has been established through a decade of ILI data collection that allows for the early detection of anomalous surges of ILI that deviate from the annual average.

With much of the research about COVID-19 happening as the pandemic unfolds, Washburne said syndromic surveillance like this shows researchers and the medical community one piece of a larger story. When coupled with COVID-19 testing efforts and serological surveys, which seek to identify the proportion of a population with immunity to an illness, this type of data collection and analysis can illuminate a piece of the puzzle that helps outline our understanding of coronavirus as a whole, he said, while also offering insight for future potential epidemics.

Washburne also said that syndromic surveillance using tools like ILINet could be applied in areas where widespread testing is too expensive.

"For communities that may not have the capacity for more large-scale testing, this may be able to help give them a picture of the movement of their epidemic in time and space," he said. "That way they can know when to implement actions like mask wearing and social distancing measures."

The practice of collecting data ahead of a potential outbreak is an investment in future public health, Washburne said. This research into COVID-19 wouldn't have been possible without the creation of the database after H1N1, so continuing to expanding the baseline data collected for other illnesses could be crucial in navigating future pandemics.

"All these different methods can be used to cross-validate each other," he said. "We know if our other methods don't work optimally, we have additional resources. Things like this can really help us be better prepared in the future."

https://www.sciencedaily.com/releases/2020/06/200626092732.htm

How to identify factors affecting COVID-19 transmission

March 26, 2020

Science Daily/Stanford University

Much remains unknown about how SARS-CoV-2, the virus that causes COVID-19, spreads through the environment. A major reason for this is that the behaviors and traits of viruses are highly variable -- some spread more easily through water, others through air; some are wrapped in layers of fatty molecules that help them avoid their host's immune system, while others are "naked."

This makes it urgent for environmental engineers and scientists to collaborate on pinpointing viral and environmental characteristics that affect transmission via surfaces, the air and fecal matter, according to Alexandria Boehm, a Stanford professor of civil and environmental engineering, and Krista Wigginton, the Shimizu Visiting Professor in Stanford's department of civil and environmental engineering and an associate professor at the University of Michigan.

Boehm and Wigginton co-authored a recently published viewpoint in Environmental Science & Technology calling for a broader, long-term and more quantitative approach to understanding viruses, such as SARS-CoV-2, that are spread through the environment. They are also principal investigators on a recently announced National Science Foundation-funded project to study the transfer of coronaviruses between skin and other materials, the effect of UV and sunlight on the coronaviruses, and the connection between disease outbreaks and virus concentrations in wastewater.

Scientists and medical experts don't have a good understanding of what virus characteristics and environmental factors control virus persistence in the environment -- for example, in aerosols and droplets, on surfaces including skin and in water including seawater, according to Boehm and Wigginton. "When a new virus emerges and poses a risk to human health, we don't have a good way of predicting how it will behave in the environment," Boehm said.

Part of the problem is historically there has been limited funding for this sort of work. The National Institutes of Health historically hasn't funded work on pathogens in the environment, and funding at the National Science Foundation for this work is limited. Also, coronaviruses and most of the emerging viruses that have caught the world's attention over the last decade are enveloped viruses that are wrapped in an outer layer of fatty lipid molecules that they've stolen from their hosts. Proteins on the surface of the envelopes can help these viruses evade the immune systems of the organisms they are infecting. "There has been much more work on the fate of non-enveloped or naked viruses because most intestinal pathogens in excrement are nonenveloped viruses -- like norovirus and rotavirus," said Wigginton.

In their paper, Boem and Wigginton address potential threats that viruses such as SARS-CoV-2 pose to water sources. We usually only worry about viruses in water if they are excreted by humans in their feces and urine. Most enveloped viruses aren't excreted in feces or urine, so they aren't usually on our minds when it comes to our water sources. There is increasing evidence that the SARS-CoV-2 viruses, or at least their genomes, are excreted in feces. If infective viruses are excreted, then fecal exposure could be a route of transmission, according to Boehm, who added, "It's unlikely this could be a major transmission route, but a person could potentially be exposed by interacting with water contaminated with untreated fecal matter."

Drinking water treatment systems have numerous treatment barriers to remove the most prevalent viruses and the most difficult-to-remove viruses, according to the engineers. Research on viruses similar to the SARS-CoV-2 virus suggests they are susceptible to these treatments. "In terms of virus concentration and persistence, this isn't a worst-case scenario," Wigginton said.

Broadly, Wigginton and Boehm write, we tend to study viruses very intensely when there is an outbreak, but the results from one virus aren't easy to extrapolate to other viruses that emerge years later. "If we took a broader approach to studying many kinds of viruses, we could better understand the characteristics driving their environmental fate," Wigginton said.

The two researchers call for experts across various fields -- including medicine and engineering and -- to work together to move methods forward faster, make discoveries and formulate strategies that wouldn't be possible independently.

https://www.sciencedaily.com/releases/2020/03/200326160759.htm