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AI model proactively predicts if a COVID-19 test might be positive or not

COVID-19 and its latest Omicron strains continue to cause infections across the country as well as globally. Serology (blood) and molecular tests are the…

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COVID-19 and its latest Omicron strains continue to cause infections across the country as well as globally. Serology (blood) and molecular tests are the two most commonly used methods for rapid COVID-19 testing. Because COVID-19 tests use different mechanisms, they vary significantly. Molecular tests measure the presence of viral SARS-CoV-2 RNA while serology tests detect the presence of antibodies triggered by the SARS-CoV-2 virus.

Credit: Florida Atlantic University

COVID-19 and its latest Omicron strains continue to cause infections across the country as well as globally. Serology (blood) and molecular tests are the two most commonly used methods for rapid COVID-19 testing. Because COVID-19 tests use different mechanisms, they vary significantly. Molecular tests measure the presence of viral SARS-CoV-2 RNA while serology tests detect the presence of antibodies triggered by the SARS-CoV-2 virus.

Currently, there is no existing study on the correlation between serology and molecular tests and which COVID-19 symptoms play a key role in producing a positive test result. A study from Florida Atlantic University’s College of Engineering and Computer Science using machine learning provides important new evidence in understanding how molecular tests versus serology tests are correlated, and what features are the most useful in distinguishing between COVID-19 positive versus test outcomes.

Researchers from the College of Engineering and Computer Science trained five classification algorithms to predict COVID-19 test results. They created an accurate predictive model using easy-to-obtain symptom features, along with demographic features such as number of days post-symptom onset, fever, temperature, age and gender.

The study demonstrates that machine-learning models, trained using simple symptom and demographic features, can help predict COVID-19 infections. Results, published in the journal Smart Health, identify the key symptom features associated with COVID-19 infection and provide a way for rapid screening and cost effective infection detection.

Findings reveal that number of days experiencing symptoms such as fever and difficulty breathing play a large role in COVID-19 test results. Findings also show that molecular tests have much narrower post-symptom onset days (between three to eight days), compared to post-symptom onset days of serology tests (between five to 38 days). As a result, the molecular test has the lowest positive rate because it measures current infection.

Furthermore, COVID-19 tests vary significantly, partially because donors’ immune response and viral load – the target of different test methods – continuously change. Even for the same donor, it might be possible to observe different positive/negative results from two types of tests.

“Molecular tests depend on viral load and serology tests depend on seroconversion, which is the period during which the body starts producing detectable levels of antibodies. Both of these tests are time dependent,” said Xingquan “Hill” Zhu, Ph.D., senior author and a professor in FAU’s Department of Electrical Engineering and Computer Science. “Our results suggest that the number of days post symptomatic are highly important for a positive COVID-19 test and should be under careful consideration when screening patients.” 

For the study, researchers used test results from 2,467 donors, each tested using one or multiple types of COVID-19 tests, which were collected as the testbed. They combined symptoms and demographic information to design a set of features for predictive modeling using the five types of machine-learning models. By cross checking test types and results, they examined the correlation between serology and molecular tests. For test outcome prediction, they labeled the 2,467 donors as positive or negative by using their serology or molecular test results, and created symptom features to represent each donor for machine learning.

“Because COVID-19 produces a wide range of symptoms and the data collection process is essentially error prone, we grouped similar symptoms into bins,” said Zhu. “Without a standardization of symptom reporting, the symptom feature space greatly increases. To combat this, we utilized this binning approach, which was able to decrease symptom feature space while keeping sample feature information.”

By using created bin features, combined with the five machine-learning algorithms, these predictive models achieved more than 81 percent AUC scores (Area under the ROC Curve, which provides an aggregate measure of performance across all possible classification thresholds), and more than 76 percent classification accuracy.

“One unique feature of our testbed is that some donors may have multiple test results, which allowed us to analyze the relationship between serology tests versus molecular tests, and also understand consistency within each type of test,” said Zhu.

The five machine learning models used by the researchers are Random Forest, XGBoost, Logistic Regression, Support Vector Machine (SVM) and Neural Network. They compared performance by using three performance metrics: Accuracy, F1-score and AUC. 

“Predictive modeling is complicated by many puzzling questions unanswered by research. The testbed created by our researchers is indeed novel and clearly shows correlation between different types of COVID-19 tests,” said Stella Batalama, Ph.D., dean, FAU College of Engineering and Computer Science. “Our researchers have designed a new way to narrow down noisy symptom features for clinical interpretation and predictive modeling. Such AI based predictive modeling approaches are becoming increasingly powerful to combat infectious diseases and many other aspects of health issues.”

Study co-author is Magdalyn E. Elkin, a Ph.D. student in FAU’s Department of Electrical Engineering and Computer Science.

This work was supported by the National Science Foundation.

– FAU –

About FAU’s College of Engineering and Computer Science:

The FAU College of Engineering and Computer Science is internationally recognized for cutting edge research and education in the areas of computer science and artificial intelligence (AI), computer engineering, electrical engineering, biomedical engineering, civil, environmental and geomatics engineering, mechanical engineering, and ocean engineering. Research conducted by the faculty and their teams expose students to technology innovations that push the current state-of-the art of the disciplines. The College research efforts are supported by the National Science Foundation (NSF), the National Institutes of Health (NIH), the Department of Defense (DOD), the Department of Transportation (DOT), the Department of Education (DOEd), the State of Florida, and industry. The FAU College of Engineering and Computer Science offers degrees with a modern twist that bear specializations in areas of national priority such as AI, cybersecurity, internet-of-things, transportation and supply chain management, and data science. New degree programs include Master of Science in AI (first in Florida), Master of Science and Bachelor in Data Science and Analytics, and the new Professional Master of Science and Ph.D. in computer science for working professionals. For more information about the College, please visit eng.fau.edu

 

About Florida Atlantic University:
Florida Atlantic University, established in 1961, officially opened its doors in 1964 as the fifth public university in Florida. Today, the University serves more than 30,000 undergraduate and graduate students across six campuses located along the southeast Florida coast. In recent years, the University has doubled its research expenditures and outpaced its peers in student achievement rates. Through the coexistence of access and excellence, FAU embodies an innovative model where traditional achievement gaps vanish. FAU is designated a Hispanic-serving institution, ranked as a top public university by U.S. News & World Report and a High Research Activity institution by the Carnegie Foundation for the Advancement of Teaching. For more information, visit www.fau.edu.

 


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The next pandemic? It’s already here for Earth’s wildlife

Bird flu is decimating species already threatened by climate change and habitat loss.

I am a conservation biologist who studies emerging infectious diseases. When people ask me what I think the next pandemic will be I often say that we are in the midst of one – it’s just afflicting a great many species more than ours.

I am referring to the highly pathogenic strain of avian influenza H5N1 (HPAI H5N1), otherwise known as bird flu, which has killed millions of birds and unknown numbers of mammals, particularly during the past three years.

This is the strain that emerged in domestic geese in China in 1997 and quickly jumped to humans in south-east Asia with a mortality rate of around 40-50%. My research group encountered the virus when it killed a mammal, an endangered Owston’s palm civet, in a captive breeding programme in Cuc Phuong National Park Vietnam in 2005.

How these animals caught bird flu was never confirmed. Their diet is mainly earthworms, so they had not been infected by eating diseased poultry like many captive tigers in the region.

This discovery prompted us to collate all confirmed reports of fatal infection with bird flu to assess just how broad a threat to wildlife this virus might pose.

This is how a newly discovered virus in Chinese poultry came to threaten so much of the world’s biodiversity.

H5N1 originated on a Chinese poultry farm in 1997. ChameleonsEye/Shutterstock

The first signs

Until December 2005, most confirmed infections had been found in a few zoos and rescue centres in Thailand and Cambodia. Our analysis in 2006 showed that nearly half (48%) of all the different groups of birds (known to taxonomists as “orders”) contained a species in which a fatal infection of bird flu had been reported. These 13 orders comprised 84% of all bird species.

We reasoned 20 years ago that the strains of H5N1 circulating were probably highly pathogenic to all bird orders. We also showed that the list of confirmed infected species included those that were globally threatened and that important habitats, such as Vietnam’s Mekong delta, lay close to reported poultry outbreaks.

Mammals known to be susceptible to bird flu during the early 2000s included primates, rodents, pigs and rabbits. Large carnivores such as Bengal tigers and clouded leopards were reported to have been killed, as well as domestic cats.

Our 2006 paper showed the ease with which this virus crossed species barriers and suggested it might one day produce a pandemic-scale threat to global biodiversity.

Unfortunately, our warnings were correct.

A roving sickness

Two decades on, bird flu is killing species from the high Arctic to mainland Antarctica.

In the past couple of years, bird flu has spread rapidly across Europe and infiltrated North and South America, killing millions of poultry and a variety of bird and mammal species. A recent paper found that 26 countries have reported at least 48 mammal species that have died from the virus since 2020, when the latest increase in reported infections started.

Not even the ocean is safe. Since 2020, 13 species of aquatic mammal have succumbed, including American sea lions, porpoises and dolphins, often dying in their thousands in South America. A wide range of scavenging and predatory mammals that live on land are now also confirmed to be susceptible, including mountain lions, lynx, brown, black and polar bears.

The UK alone has lost over 75% of its great skuas and seen a 25% decline in northern gannets. Recent declines in sandwich terns (35%) and common terns (42%) were also largely driven by the virus.

Scientists haven’t managed to completely sequence the virus in all affected species. Research and continuous surveillance could tell us how adaptable it ultimately becomes, and whether it can jump to even more species. We know it can already infect humans – one or more genetic mutations may make it more infectious.

At the crossroads

Between January 1 2003 and December 21 2023, 882 cases of human infection with the H5N1 virus were reported from 23 countries, of which 461 (52%) were fatal.

Of these fatal cases, more than half were in Vietnam, China, Cambodia and Laos. Poultry-to-human infections were first recorded in Cambodia in December 2003. Intermittent cases were reported until 2014, followed by a gap until 2023, yielding 41 deaths from 64 cases. The subtype of H5N1 virus responsible has been detected in poultry in Cambodia since 2014. In the early 2000s, the H5N1 virus circulating had a high human mortality rate, so it is worrying that we are now starting to see people dying after contact with poultry again.

It’s not just H5 subtypes of bird flu that concern humans. The H10N1 virus was originally isolated from wild birds in South Korea, but has also been reported in samples from China and Mongolia.

Recent research found that these particular virus subtypes may be able to jump to humans after they were found to be pathogenic in laboratory mice and ferrets. The first person who was confirmed to be infected with H10N5 died in China on January 27 2024, but this patient was also suffering from seasonal flu (H3N2). They had been exposed to live poultry which also tested positive for H10N5.

Species already threatened with extinction are among those which have died due to bird flu in the past three years. The first deaths from the virus in mainland Antarctica have just been confirmed in skuas, highlighting a looming threat to penguin colonies whose eggs and chicks skuas prey on. Humboldt penguins have already been killed by the virus in Chile.

A colony of king penguins.
Remote penguin colonies are already threatened by climate change. AndreAnita/Shutterstock

How can we stem this tsunami of H5N1 and other avian influenzas? Completely overhaul poultry production on a global scale. Make farms self-sufficient in rearing eggs and chicks instead of exporting them internationally. The trend towards megafarms containing over a million birds must be stopped in its tracks.

To prevent the worst outcomes for this virus, we must revisit its primary source: the incubator of intensive poultry farms.

Diana Bell does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.

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A major cruise line is testing a monthly subscription service

The Cruise Scarlet Summer Season Pass was designed with remote workers in mind.

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While going on a cruise once meant disconnecting from the world when between ports because any WiFi available aboard was glitchy and expensive, advances in technology over the last decade have enabled millions to not only stay in touch with home but even work remotely.

With such remote workers and digital nomads in mind, Virgin Voyages has designed a monthly pass that gives those who want to work from the seas a WFH setup on its Scarlet Lady ship — while the latter acronym usually means "work from home," the cruise line is advertising as "work from the helm.”

Related: Royal Caribbean shares a warning with passengers

"Inspired by Richard Branson's belief and track record that brilliant work is best paired with a hearty dose of fun, we're welcoming Sailors on board Scarlet Lady for a full month to help them achieve that perfect work-life balance," Virgin Voyages said in announcing its new promotion. "Take a vacation away from your monotonous work-from-home set up (sorry, but…not sorry) and start taking calls from your private balcony overlooking the Mediterranean sea."

A man looks through his phone while sitting in a hot tub on a cruise ship.

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This is how much it'll cost you to work from a cruise ship for a month

While the single most important feature for successful work at sea — WiFi — is already available for free on Virgin cruises, the new Scarlet Summer Season Pass includes a faster connection, a $10 daily coffee credit, access to a private rooftop, and other member-only areas as well as wash and fold laundry service that Virgin advertises as a perk that will allow one to concentrate on work

More Travel:

The pass starts at $9,990 for a two-guest cabin and is available for four monthlong cruises departing in June, July, August, and September — each departs from ports such as Barcelona, Marseille, and Palma de Mallorca and spends four weeks touring around the Mediterranean.

Longer cruises are becoming more common, here's why

The new pass is essentially a version of an upgraded cruise package with additional perks but is specifically tailored to those who plan on working from the ship as an opportunity to market to them.

"Stay connected to your work with the fastest at-sea internet in the biz when you want and log-off to let the exquisite landscape of the Mediterranean inspire you when you need," reads the promotional material for the pass.

Amid the rise of remote work post-pandemic, cruise lines have been seeing growing interest in longer journeys in which many of the passengers not just vacation in the traditional sense but work from a mobile office.

In 2023, Turkish cruise line operator Miray even started selling cabins on a three-year tour around the world but the endeavor hit the rocks after one of the engineers declared the MV Gemini ship the company planned to use for the journey "unseaworthy" and the cruise ship line dealt with a PR scandal that ultimately sank the project before it could take off.

While three years at sea would have set a record as the longest cruise journey on the market, companies such as Royal Caribbean  (RCL) (both with its namesake brand and its Celebrity Cruises line) have been offering increasingly long cruises that serve as many people’s temporary homes and cross through multiple continents.

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As the pandemic turns four, here’s what we need to do for a healthier future

On the fourth anniversary of the pandemic, a public health researcher offers four principles for a healthier future.

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John Gomez/Shutterstock

Anniversaries are usually festive occasions, marked by celebration and joy. But there’ll be no popping of corks for this one.

March 11 2024 marks four years since the World Health Organization (WHO) declared COVID-19 a pandemic.

Although no longer officially a public health emergency of international concern, the pandemic is still with us, and the virus is still causing serious harm.

Here are three priorities – three Cs – for a healthier future.

Clear guidance

Over the past four years, one of the biggest challenges people faced when trying to follow COVID rules was understanding them.

From a behavioural science perspective, one of the major themes of the last four years has been whether guidance was clear enough or whether people were receiving too many different and confusing messages – something colleagues and I called “alert fatigue”.

With colleagues, I conducted an evidence review of communication during COVID and found that the lack of clarity, as well as a lack of trust in those setting rules, were key barriers to adherence to measures like social distancing.

In future, whether it’s another COVID wave, or another virus or public health emergency, clear communication by trustworthy messengers is going to be key.

Combat complacency

As Maria van Kerkove, COVID technical lead for WHO, puts it there is no acceptable level of death from COVID. COVID complacency is setting in as we have moved out of the emergency phase of the pandemic. But is still much work to be done.

First, we still need to understand this virus better. Four years is not a long time to understand the longer-term effects of COVID. For example, evidence on how the virus affects the brain and cognitive functioning is in its infancy.

The extent, severity and possible treatment of long COVID is another priority that must not be forgotten – not least because it is still causing a lot of long-term sickness and absence.

Culture change

During the pandemic’s first few years, there was a question over how many of our new habits, from elbow bumping (remember that?) to remote working, were here to stay.

Turns out old habits die hard – and in most cases that’s not a bad thing – after all handshaking and hugging can be good for our health.

But there is some pandemic behaviour we could have kept, under certain conditions. I’m pretty sure most people don’t wear masks when they have respiratory symptoms, even though some health authorities, such as the NHS, recommend it.

Masks could still be thought of like umbrellas: we keep one handy for when we need it, for example, when visiting vulnerable people, especially during times when there’s a spike in COVID.

If masks hadn’t been so politicised as a symbol of conformity and oppression so early in the pandemic, then we might arguably have seen people in more countries adopting the behaviour in parts of east Asia, where people continue to wear masks or face coverings when they are sick to avoid spreading it to others.

Although the pandemic led to the growth of remote or hybrid working, presenteeism – going to work when sick – is still a major issue.

Encouraging parents to send children to school when they are unwell is unlikely to help public health, or attendance for that matter. For instance, although one child might recover quickly from a given virus, other children who might catch it from them might be ill for days.

Similarly, a culture of presenteeism that pressures workers to come in when ill is likely to backfire later on, helping infectious disease spread in workplaces.

At the most fundamental level, we need to do more to create a culture of equality. Some groups, especially the most economically deprived, fared much worse than others during the pandemic. Health inequalities have widened as a result. With ongoing pandemic impacts, for example, long COVID rates, also disproportionately affecting those from disadvantaged groups, health inequalities are likely to persist without significant action to address them.

Vaccine inequity is still a problem globally. At a national level, in some wealthier countries like the UK, those from more deprived backgrounds are going to be less able to afford private vaccines.

We may be out of the emergency phase of COVID, but the pandemic is not yet over. As we reflect on the past four years, working to provide clearer public health communication, avoiding COVID complacency and reducing health inequalities are all things that can help prepare for any future waves or, indeed, pandemics.

Simon Nicholas Williams has received funding from Senedd Cymru, Public Health Wales and the Wales Covid Evidence Centre for research on COVID-19, and has consulted for the World Health Organization. However, this article reflects the views of the author only, in his academic capacity at Swansea University, and no funding or organizational bodies were involved in the writing or content of this article.

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