Sorting out viruses with machine learning

November 11, 2020

Osaka, Japan - The ongoing global pandemic has created an urgent need for rapid tests that can diagnose the presence of the SARS-CoV-2 virus, the pathogen that causes COVID-19, and distinguish it from other respiratory viruses. Now, researchers from Japan have demonstrated a new system for single-virion identification of common respiratory pathogens using a machine learning algorithm trained on changes in current across silicon nanopores. This work may lead to fast and accurate screening tests for diseases like COVID-19 and influenza.

In a study published this month in ACS Sensors scientists at Osaka University have introduced a new system using silicon nanopores sensitive enough to detect even a single virus particle when coupled with a machine learning algorithm.

In this method, a silicon nitride layer just 50 nm thick suspended on a silicon wafer has tiny nanopores added, which are themselves only 300 nm in diameter. When a voltage difference is applied to the solution on either side of the wafer, ions travel through the nanopores in a process called electrophoresis.

The motion of the ions can be monitored by the current they generate, and when a viral particle enters a nanopore, it blocks some of the ions from passing through, leading to a transient dip in current. Each dip reflects the physical properties of the particle, such as volume, surface charge, and shape, so they can be used to identify the kind of virus.

The natural variation in the physical properties of virus particles had previously hindered implementation of this approach, however, using machine learning, the team built a classification algorithm trained with signals from known viruses to determine the identity of new samples. "By combining single-particle nanopore sensing with artificial intelligence, we were able to achieve highly accurate identification of multiple viral species," explains senior author Makusu Tsutsui.

The computer can discriminate the differences in electrical current waveforms that cannot be identified by human eyes, which enables highly accurate virus classification. In addition to coronavirus, the system was tested with similar pathogens - respiratory syncytial virus, adenovirus, influenza A, and influenza B.

The team believes that coronaviruses are especially well suited for this technique since their spiky outer proteins may even allow different strains to be classified separately. "This work will help with the development of a virus test kit that outperforms conventional viral inspection methods," says last author Tomoji Kawai.

Compared with other rapid viral tests like polymerase chain reaction or antibody-based screens, the new method is much faster and does not require costly reagents, which may lead to improved diagnostic tests for emerging viral particles that cause infectious diseases such as COVID-19.
The article, "Digital pathology platform for respiratory tract infection diagnosis via multiplex single-particle detections," was published in ACS Sensors at DOI:

About Osaka University

Osaka University was founded in 1931 as one of the seven imperial universities of Japan and is now one of Japan's leading comprehensive universities with a broad disciplinary spectrum. This strength is coupled with a singular drive for innovation that extends throughout the scientific process, from fundamental research to the creation of applied technology with positive economic impacts. Its commitment to innovation has been recognized in Japan and around the world, being named Japan's most innovative university in 2015 (Reuters 2015 Top 100) and one of the most innovative institutions in the world in 2017 (Innovative Universities and the Nature Index Innovation 2017). Now, Osaka University is leveraging its role as a Designated National University Corporation selected by the Ministry of Education, Culture, Sports, Science and Technology to contribute to innovation for human welfare, sustainable development of society, and social transformation.


Osaka University

Related Infectious Diseases Articles from Brightsurf:

Understanding the spread of infectious diseases
Physicists at M√ľnster University (Germany) have shown in model simulations that the COVID-19 infection rates decrease significantly through social distancing.

Forecasting elections with a model of infectious diseases
Election forecasting is an innately challenging endeavor, with results that can be difficult to interpret and may leave many questions unanswered after close races unfold.

COVID-19 a reminder of the challenge of emerging infectious diseases
The emergence and rapid increase in cases of coronavirus disease 2019 (COVID-19), a respiratory illness caused by a novel coronavirus, pose complex challenges to the global public health, research and medical communities, write federal scientists from NIH's National Institute of Allergy and Infectious Diseases (NIAID) and from the Centers for Disease Control and Prevention (CDC).

Certain antidepressants could provide treatment for multiple infectious diseases
Some antidepressants could potentially be used to treat a wide range of diseases caused by bacteria living within cells, according to work by researchers in the Virginia Commonwealth University School of Medicine and collaborators at other institutions.

Opioid epidemic is increasing rates of some infectious diseases
The US faces a public health crisis as the opioid epidemic fuels growing rates of certain infectious diseases, including HIV/AIDS, hepatitis, heart infections, and skin and soft tissue infections.

Infectious diseases could be diagnosed with smartphones in sub-Saharan Africa
A new Imperial-led review has outlined how health workers could use existing phones to predict and curb the spread of infectious diseases.

The Lancet Infectious Diseases: Experts warn of a surge in vector-borne diseases as humanitarian crisis in Venezuela worsens
The ongoing humanitarian crisis in Venezuela is accelerating the re-emergence of vector-borne diseases such as malaria, Chagas disease, dengue, and Zika virus, and threatens to jeopardize public health gains in the country over the past two decades, warn leading public health experts.

Glow-in-the-dark paper as a rapid test for infectious diseases
Researchers from Eindhoven University of Technology (The Netherlands) and Keio University (Japan) present a practicable and reliable way to test for infectious diseases.

Math shows how human behavior spreads infectious diseases
Mathematics can help public health workers better understand and influence human behaviors that lead to the spread of infectious disease, according to a study from the University of Waterloo.

Many Americans say infectious and emerging diseases in other countries will threaten the US
An overwhelming majority of Americans (95%) think infectious and emerging diseases facing other countries will pose a 'major' or 'minor' threat to the U.S. in the next few years, but more than half (61%) say they are confident the federal government can prevent a major infectious disease outbreak in the US, according to a new national public opinion survey commissioned by Research!America and the American Society for Microbiology.

Read More: Infectious Diseases News and Infectious Diseases Current Events is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to