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 covid-19 testing


Senior Data Analyst-FHIR

#artificialintelligence

We are looking for an energetic and self-motivated individual to help us rollout our health plan in Austin and to collaborate with our data partners. Co-founded by CEO Fred Turner and powered by a team of world-leading doctors, scientists, engineers, and health industry experts, Curative responded in March 2020 to the urgent need for COVID-19 testing, ultimately developing a network of thousands of testing sites across over 40 states and three CLIA-certified, high-complexity laboratories. As a result, Curative and its managed medical entities provided over 30 million COVID-19 tests and over 2 million COVID-19 vaccines. Curative's patient-facing services, healthcare facilities, integrated supply chain, and labs are part of a large platform we've built from the ground up that has allowed us to grow quickly and more efficiently than other healthcare companies. As a result, we were one of the first companies to respond to the pandemic providing COVID-19 testing at scale across the United States.


Should Parents Stock Up on At-Home COVID Tests?

Slate

He's 11-years-old and, until he can receive his shots, Gronvall's been using at-home COVID-19 test kits in order to determine if his sniffles are more than allergies or a slight cold. The test swabs are longer than a Q-tip, but easier on the nasal cavity than a flu diagnostic or the original "brain swab" used to test for COVID since early in the pandemic. "There's often a lot of stuff coming out of their nose," Gronvall said of her kids, with a slight chuckle, when we talked recently. As an associate professor at the Johns Hopkins Bloomberg School of Public Health, Gronvall knows the importance of testing. "We can't all rely on everybody being extra scrupulous and paying attention to all of the COVID restrictions," she said.


Japan eyes use of robots to boost COVID-19 testing as Olympics loom

The Japan Times

Health minister Norihisa Tamura watched a demonstration Tuesday of a prototype automated COVID-19 testing machine that uses a robotic arm to take a sample from a person's nose and can deliver the results in about 80 minutes. The robot system, built by Kawasaki Heavy Industries Inc., fits in a standard shipping container that can be transported by truck and set up at stadiums, theme parks and other mass gatherings, the company said. "Looking at the global trend, we need to increase the number of people receiving tests, and the demand for preventive testing is rising," Tamura told reporters at the demonstration. Prime Minister Yoshihide Suga's administration has attracted criticism for Japan's paucity of testing. His government is under pressure to show it has the pandemic under control with fewer than 200 days until the start of the Summer Olympics in Tokyo -- already delayed by a year -- and vaccinations yet to start.


COVID-19 testing: One size does not fit all

Science

Tests for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were developed within days of the release of the virus genome ([ 1 ][1]). Multiple countries have been successful at controlling SARS-CoV-2 transmission by investing in large-scale testing capacity ([ 2 ][2]). Most testing has focused on quantitative polymerase chain reaction (qPCR) assays, which are capable of detecting minute amounts of viral RNA. Although powerful, these molecular tools cannot be scaled to meet demands for more extensive public health testing. To combat COVID-19, the “one-size-fits-all” approach that has dominated and confused decision-making with regard to testing and the evaluation of tests is unsuitable: Diagnostics, screening, and surveillance serve different purposes, demand distinct strategies, and require separate approval mechanisms. By supporting the innovation, approval, manufacturing, and distribution of simpler and cheaper screening and surveillance tools, it will be possible to more effectively limit the spread of COVID-19 and respond to future pandemics. Many types of tests are available for COVID-19 for clinical and public health use (see the figure). Testing can be performed in a central laboratory, at the point of care (POC), or in the community at the workplace, school, or home. COVID-19 testing begins with specimen collection. For medical use, a nasopharyngeal swab collected by a health care professional has been used for detection of virus infections. Demands on testing throughput for COVID-19, however, have driven new collection approaches, including saliva and less invasive nasal swabs. COVID-19 tests include molecular tests such as qPCR, isothermal amplification, and CRISPR, as well as antigen tests that detect SARS-CoV-2 proteins directly. Although rapid antigen tests have lower analytical sensitivity (i.e., require greater amounts of virus material to turn positive) than qPCR-based tests, their ability to detect infectious individuals with culturable virus is as high as for qPCR ([ 3 ][3]). Specificity (i.e., correctly identifying those not infected with SARS-CoV-2) of antigen tests achieves comparable results to molecular tests ([ 4 ][4]). Diagnostic testing for COVID-19 focuses on accurately identifying patients who are infected with SARS-CoV-2 to establish the presence or absence of disease and is performed on symptomatic patients or asymptomatic individuals who are at high risk of infection. This type of testing requires assays that are highly sensitive, so as to not miss COVID-19 patients (false negatives), and specific, so as to not wrongly diagnose SARS-CoV-2–negative individuals as having COVID-19 (false positives). These tests are typically performed by centralized high-complexity laboratories with specialized equipment using qPCR assays, with results that can be reported within 12 to 48 hours. Major bottlenecks in testing, however, have led to turnaround times exceeding 5 to 10 days in some regions, making such tests useless to prevent transmission. POC diagnostic testing at medical facilities can be qPCR assays, isothermal amplification, or antigen-based ([ 4 ][4]). These POC tests often require instruments that run a limited number of tests and can return results in under an hour. The need for an instrument limits the number of tests that can be performed and where they can be used. However, newer antigen tests are becoming available that do not require instruments or skilled operators, potentially allowing for much more distributed POC testing. Surveillance testing of populations can be used both as a tool for understanding historical exposures and as a measure of ongoing community transmission. For the former, serological testing of individuals for the presence of SARS-CoV-2–specific antibodies is used to identify those previously infected. For the latter, surveillance testing can be an effective way to monitor real-time SARS-CoV-2 spread in communities. One promising method is wastewater surveillance, which has been used to assess community transmission of poliovirus ([ 5 ][5]) and has shown potential for COVID-19 ([ 6 ][6]). qPCR testing of wastewater is used to detect SARS-CoV-2, and frequency dynamics of viral genetic material indicate COVID-19 infections in a community. Surveillance can also be performed from swab or saliva samples taken directly from individuals, and, in populations with low COVID-19 prevalence, pooling can be used to increase capacity and lower cost. For surveillance testing, the goal is not identification of every case but rather the collection of data from representative samples that accurately measure prevalence and serve to inform public health policy and resource allocation. Because the focus is on extrapolations to the population and not the individual, tests with known deviations from 100% sensitivity and specificity are still appropriate when the variance can be statistically corrected ([ 7 ][7]). To be most effective, results should include reported qPCR cycle thresholds, which is an estimate of viral load ([ 7 ][7]), to model epidemic trajectory and allow for real-time evaluation of mitigation programs ([ 8 ][8]), including once vaccination programs have begun. Screening testing of asymptomatic individuals to detect people who are likely infectious has been critically underused yet is one of the most promising tools to combat the COVID-19 pandemic ([ 9 ][9]). Infection with SARS-CoV-2 does not lead to symptoms in ∼20 to 40% of cases, and symptomatic disease is preceded by a presymptomatic incubation period ([ 10 ][10]). However, asymptomatic and presymptomatic cases are key contributors to virus spread, complicating our ability to break transmission chains ([ 10 ][10]). Entry screening to detect infectious individuals before accessing facilities (e.g., nursing homes, restaurants, and airports), along with symptom screening and temperature checks, can be beneficial, particularly in high-risk facilities such as skilled nursing facilities. When used strategically, entry-screening measures can be effective at suppressing transmission. Entry screening requires testing that provides rapid results—ideally within 15 min—to be most effective. The required sensitivity and specificity of entry-screening tests are, like all tests, context dependent. Entry-screening tests for a nursing home, for example, must be highly sensitive because the consequences of bringing SARS-CoV-2 into a nursing home can be devastating. Such tests must also be highly specific because the consequences of grouping a false-positive person with COVID-19–positive individuals could be deadly. Conversely, because children have substantially reduced mortality from COVID-19, entry screening into schools might require greater compromise that balances resources and sensitivity to test as many individuals as possible with a need to minimize disruptive false positives. Key to use of tests for entrance screening is that a negative test alone should not be considered sufficient to enter—that should be based on satisfying other requirements, including masks and physical distancing. Conversely, a positive test should be sufficient to bar entry in most settings. Public health screening is potentially the most powerful form of COVID-19 testing, aimed at outbreak suppression through maximizing detection of infectious individuals. This type of screening entails frequent serial testing of large fractions of the population, through self-administered at-home rapid tests, or in the community at high-contact settings, such as schools and workplaces ([ 9 ][9]). Public health screening can achieve herd effects by stopping onward spread through detection of asymptomatic or presymptomatic cases (fig. S1). Notably, not every transmission chain needs to be severed to achieve herd effects. Mathematical models that incorporate relevant variation in viral loads and test accuracy suggest that with frequent testing of a large fraction of a population, a sufficient number of cases could be detected to create herd effects ([ 11 ][11]). For example, Slovakia undertook public health screening to address COVID-19 ([ 12 ][12]): During a 2-week period, ∼80% of the population was screened using rapid antigen tests. With 50,000 cases identified, combined with other public health measures, it reduced incidence by 82% within 2 weeks ([ 12 ][12]). An important feature of large-scale public health screening is that centrally controlled reporting and contact tracing programs are not essential to induce herd effects as they are for surveillance testing. In a robust public health screening program, sufficient numbers of people are routinely testing themselves, such that contact tracing is subsumed by the screening program ([ 11 ][11]). Similar to home pregnancy tests, screening tests should be easy to obtain and administer, fast, and cheap. Like diagnostic tests, these tests must produce very low false-positive rates. If a screening test does not achieve high-enough specificity (e.g., >99.9%), screening programs can be paired with secondary confirmatory testing. Unlike diagnostic tests, however, the sensitivity of screening tests should not be determined based on their ability to diagnose patients but rather by their ability to accurately identify people who are most at risk of transmitting SARS-CoV-2. Such individuals tend to have higher viral loads ([ 13 ][13]), which makes the virus easier to detect ([ 14 ][14]). A focus on identifying infectious people means that frequency and abundance of tests should be prioritized above achieving high analytical sensitivity ([ 11 ][11]). Indeed, loss in sensitivity of individual tests, within reason, can be compensated for by frequency of testing and wider dissemination of tests ([ 9 ][9]). In addition, public health messaging should ensure appropriate expectations of screening, particularly around sensitivity and specificity so that false negatives and false positives do not erode public trust. ![Figure][15] COVID-19 testing strategies Testing for SARS-CoV-2 can be for personal or population health. Collection can be from symptomatic or asymptomatic individuals, as well as from wastewater and swabs of surfaces. The tests may be performed in central laboratories, at the POC, or using rapid tests. Attributes of tests differ according to application. GRAPHIC: KELLIE HOLOSKI/ SCIENCE Tests for public health screening require rapid, decentralized solutions that can be scaled for frequent screening of large numbers of asymptomatic individuals. Lateral-flow antigen tests and upcoming paper-based synthetic biology and CRISPR-based assays fit these needs and could be scaled to tens of millions of daily tests ([ 9 ][9]). These tests are simple and cheap, can be self-administered, and do not require machines to run and return results. The Abbott BinaxNOW rapid antigen test, which recently received an Emergency Use Authorization (EUA) in the United States as a diagnostic device, also comes with a smartphone app, allowing self-reporting of COVID-19 status that could be used instead of centralized reporting by public health agencies. Critically, despite being shown to be highly effective at detecting infectious individuals ([ 14 ][14]), very few of these tests are currently approved for screening of asymptomatic individuals, substantially limiting their utility. If such tests were made available direct to consumer (priced to allow equitable access) or produced and provided free of charge by governments, individuals could obtain their COVID-19 status at their own choosing and without complex medical decisions. Testing is a central pillar of clinical and public health response to global health emergencies, including the COVID-19 pandemic. Nearly all testing modalities have a role, and the one-size-fits-all approach to testing by many Western countries has failed. Many lower- and middle-income countries—including Senegal, Vietnam, and Ghana—have fared far better in their COVID-19 response, often using strong testing programs. The focus on diagnostic tests and the use of preexisting authorization pathways focused on qPCR-based clinical diagnostics not only slows the development and deployment of new surveillance and screening tests but also confuses the picture of what metrics effective public health tools should achieve. Testing to diagnose a patient with COVID-19 is fundamentally different from testing a person to prevent onward transmission. Regulatory pathways should be modified to incorporate these differences so that public health and screening tests are appropriately evaluated. It is necessary to be innovative and produce, distribute, and continuously improve the tests that exist to save lives and gain control of the COVID-19 pandemic. [science.sciencemag.org/content/371/6525/126/suppl/DC1][16] 1. [↵][17]1. V. M. Corman et al ., Euro. Surveill. 25, 2000045 (2020). [OpenUrl][18][CrossRef][19][PubMed][20] 2. [↵][21]1. M. G. Baker et al ., N. Engl. J. Med. 383, e56 (2020). [OpenUrl][22][CrossRef][23][PubMed][24] 3. [↵][25]1. A. Pekosz et al ., medRxiv 10.1101/2020.10.02.20205708 (2020). 4. [↵][26]1. R. Weissleder et al ., Sci. Transl. Med. 12, abc1931 (2020). [OpenUrl][27][CrossRef][28] 5. [↵][29]1. H. Asghar et al ., J. Infect. Dis. 210, S294 (2014). [OpenUrl][30][CrossRef][31][PubMed][32] 6. [↵][33]1. A. Nemudryi et al ., Cell Rep. Med. 1, 100098 (2020). [OpenUrl][34][CrossRef][35][PubMed][36] 7. [↵][37]1. R. Kahn et al ., medRxiv 10.1101/2020.05.02.20088765 (2020). 8. [↵][38]1. J. A. Hay et al ., medRxiv 10.1101/2020.10.08.20204222 (2020). 9. [↵][39]1. M. J. Mina et al ., N. Engl. J. Med. 383, e120 (2020). [OpenUrl][40][PubMed][41] 10. [↵][42]1. X. He et al ., Nat. Med. 26, 672 (2020). [OpenUrl][43][CrossRef][44][PubMed][41] 11. [↵][45]1. D. B. Larremore et al ., Sci. Adv. 10.1126/sciadv.abd5393 (2020). 12. [↵][46]1. M. Pavelka et al ., “The effectiveness of population-wide, rapid antigen test based screening in reducing SARS-CoV-2 infection prevalence in Slovakia,” CMMID Repository, 11 November 2020; . 13. [↵][47]1. E. A. Meyerowitz et al ., Ann. Intern. Med. 10.7326/M20-5008 (2020). 14. [↵][48]1. V. M. Corman et al ., medRxiv 10.1101/2020.11.12.20230292 (2020). 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AI system bests radiologists in spotting COVID-19 in lungs

#artificialintelligence

A new artificial intelligence (AI) platform developed by Northwestern University researchers can detect COVID-19 in the lungs 10 times faster and a bit more accurately than specialized cardiothoracic radiologists, according to a study published today in Radiology. The researchers trained and tested DeepCOVID-XR, a machine-learning algorithm that analyzes chest X-rays, on 17,002 X-ray images, 5,445 of them with signs of COVID-19, collected from February to April. When pitted against five experienced cardiothoracic radiology subspecialists, DeepCOVID-XR analyzed each of 300 randomly selected test images in about 18 minutes, versus the 2.5 to 3.5 hours of individual radiologists. DeepCOVID-XR was 82% accurate, compared with the radiologists' 76% to 81% individually and 81% as a team. "These are experts who are sub-specialty trained in reading chest imaging, whereas the majority of chest X-rays are read by general radiologists or initially interpreted by non-radiologists, such as the treating clinician," lead author Ramsey Wehbe, MD, said in a Northwestern news release.


Shipping containers could be converted into automated COVID-19 laboratories

Daily Mail - Science & tech

'Portable coronavirus labs' built into shipping containers which can be moved about on a truck could provide a new low-cost way to process COVID-19 tests. The team say it is the first fully functional lab that can be'immediately deployed anywhere in the world' for coronavirus testing and can process 2,400 tests per day. The system uses low-cost liquid handling robots to detect the presence of the SARS-CoV-2 virus in samples submitted for testing by the public. 'Portable coronavirus labs' built into shipping containers which can be moved about on a truck could provide a new low-cost way to process COVID-19 tests. Called CONTAIN, it's an open source design using supplies and agents not owned by any one company - meaning it doesn't have the same supply chain constraints as other coronavirus testing services.


Coronavirus Update: GOP Senators Disagree With Trump On COVID-19 Testing, 'There Are Still Shortfalls'

International Business Times

Republican senators are saying out loud the extent of mass testing for COVID-19 in the United States isn't where it should be -- not by a long shot -- and contradict president Donald Trump's oft repeated claims the U.S. has so much testing available. "We have so much testing," claimed Trump Thursday. Mass testing is one of the only few known ways to end the COVID-19 pandemic in this country. The U.S. has conducted only 8.1 million tests since February. The White House says its goal is two million tests per week per state by the end of May.


How false negatives are complicating COVID-19 testing

The Japan Times

Washington – As COVID-19 tests become more widely available across the U.S., scientists have warned about a growing concern: Many people with negative results might actually have the virus. That could have devastating implications as a global recession looms and governments wrangle with the question of when to reopen economies shuttered with billions of people ordered to stay home in an effort to stop transmissions of the deadly disease. The majority of tests around the world use a technology called PCR, which detects pieces of the coronavirus in mucus samples. But "there are a lot of things that impact whether or not the test actually picks up the virus," said Priya Sampathkumar, an infectious diseases specialist at Mayo Clinic in Minnesota. "It depends on how much virus the person is shedding (through sneezing, coughing and other bodily functions), how the test was collected and whether it was done appropriately by someone used to collecting these swabs, and then how long it sat in transport," she said.