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Juan Lama
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The Omicron variant is characterised by more than 50 distinct mutations, the majority of which are located in the spike protein. The implications of these mutations for disease transmission, tissue tropism and diagnostic testing are still to be determined. We evaluated the relative performance of saliva and mid-turbinate swabs as RT-PCR samples for the Delta and Omicron variants. The positive percent agreement (PPA) of saliva swabs and mid-turbinate swabs to a composite standard was 71% (95% CI: 53-84%) and 100% (95% CI: 89-100%), respectively, for the Delta variant. However, for the Omicron variant saliva and mid-turbinate swabs had a 100% (95% CI: 90-100%) and 86% (95% CI: 71-94%) PPA, respectively. This finding supports ex-vivo data of altered tissue tropism from other labs for the Omicron variant. Reassessment of the diagnostic testing standard-of-care may be required as the Omicron variant becomes the dominant variant worldwide. Preprint available at medRxiv (Dec. 24, 2021): https://doi.org/10.1101/2021.12.22.21268246
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Juan Lama
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In a small study in San Francisco, Abbott’s BinaxNOW identified infectious people nearly as accurately as a P.C.R. test. A $5 rapid test for the coronavirus may be nearly as effective as the slower, more complex polymerase chain reaction test for identifying people who may spread the coronavirus, a novel experiment has found. The study, conducted by scientists at the University of California, San Francisco, is among the first head-to-head comparisons of a rapid test and the P.C.R. diagnostic tool under real-world conditions. But the number of participants was comparatively small, and the data have not been peer-reviewed or published. A rapid test still cannot conclusively determine that an individual is not infected; the tests are intended primarily to detect the presence of high levels of the virus, rather than its absence, and are authorized only to evaluate symptomatic people. At the moment, anyone who has been exposed to the virus should be tested by P.C.R., said Joseph DeRisi, an infectious disease expert at U.C.S.F. and a co-leader of the project. At the moment, anyone who has been exposed to the virus should be tested by P.C.R., said Joseph DeRisi, an infectious disease expert at U.C.S.F. and a co-leader of the project. The new test, Abbott’s BinaxNOW, offers results in 15 minutes, compared with the days or weeks people may have to wait for a P.C.R. result. The Trump administration already has purchased 150 million BinaxNOW tests and plans to ship them to states for use in schools, nursing homes and meatpacking plants. The tests could also be used to screen people in communities where time, trust and resources are in short supply. The study assessed the BinaxNOW in one such community, a largely Latino neighborhood in San Francisco. On three mornings in late September, as commuters emerged from a BART train station in the Mission District, they were offered two nasal swabs: one for a P.C.R. test, the other for the rapid test with a simple readout. The commuters received only the P.C.R. result, by text, but the researchers compared both tests. Of the 878 people who took the tests at the train station, only 26 tested positive on the researchers’ P.C.R. BinaxNOW identified only 15 of them. But many experts have argued that the P.C.R. test is too sensitive, picking up fragments of the coronavirus lingering in the body long after people have recovered and are no longer infectious. A study by the company Becton Dickinson recently showed that rapid tests correlated better with live virus than P.C.R. But when they only considered P.C.R. results that corresponded to high viral loads, the researchers found that the BinaxNOW test detected 15 of the 16 people who were most likely to transmit the virus... Preprint available at medRxiv (October 5, 2020): https://doi.org/10.1101/2020.10.02.20205708
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Juan Lama
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Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The most widely used method of COVID-19 diagnostics is a reverse transcription polymerase chain reaction (RT-PCR) assay, to detect the presence of SARS-CoV-2 RNA in patient samples, typically from nasopharyngeal swabs. RNA extraction is a major bottleneck in current COVID-19 testing, in terms of turn-around, logistics, component availability and cost, which delays or completely precludes COVID-19 diagnostics in many settings. Efforts to simplify the current methods are critical, as increased diagnostic availability and efficiency would benefit patient care and infection control. Here, we describe methods to circumvent RNA extraction in COVID-19 testing by performing RT-PCR directly on heat-inactivated subject samples as well as samples lysed with readily available detergents. Our data, including benchmarking with 597 clinically diagnosed patient samples against a standardised and sensitive diagnostic system, show that direct RT-PCR is a viable option to extraction-based COVID-19 diagnostics. Furthermore, using controlled amounts of active SARS-CoV-2, we evaluated performance of generic buffers as sample medium for the direct RT-PCR assay, identifying several suitable formulations. We also confirmed the effectiveness of heat inactivation of SARS-CoV-2 by plaque assay. Significant savings in terms of time and cost can be achieved by embracing RNA-extraction-free protocols, that feed directly into the established PCR-based testing pipeline. This could aid the expansion of COVID-19 testing. Preprint in medRxiv (August 5, 2020): https://doi.org/10.1101/2020.04.17.20067348
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Juan Lama
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The startup says its compact, point-of-care test can deliver rapid results, compared with hours or days at centralized labs. Mesa Biotech, a privately held San Diego startup that designs point-of-care flu tests, has received emergency authorization from federal authorities to provide a molecular test for the COVID-19 coronavirus. The company, which employs 50 workers, said its palm-size COVID-19 tests deliver results in as little as 30 minutes. That is significantly faster than the hours or days it can take to get results from centralized labs. The U.S. Food and Drug Administration authorized Mesa’s test for use in moderate to highly complex medical labs, as well as other health settings with trained professionals such as emergency rooms or clinics, said Steven Sepulveda, a vice president of global business development. “What they wanted to do was really broaden where (testing) is done,” said Sepulveda. “Now it is done in central labs. This gets it closer to the patient, in the ER, etc.” Mesa is the second point-of-care test provider to receive FDA emergency authorization for COVID-19. Cepheid, a Bay Area subsidiary of global life sciences firm Danaher, gained approval for its a 45-minute test last week. Delays in testing have hindered the fight against the coronavirus pandemic in the U.S. Efforts to break the bottleneck include bringing more coronavirus tests from private companies to the fight. Several diagnostic companies with operations in the San Diego region, including GenMark Diagnostics, Quidel Corp., Hologic and Thermo Fisher, recently received emergency approval to provide coronavirus tests to labs. Mesa designed its rapid test with the help of a $561,000 contract from the U.S. Department of Health and Human Services. The company already has approved point-of-care tests for Flu A/B available in the U.S. through a distribution partnership with Sekisui Diagnostics. Mesa said it is ready to ship coronavirus tests immediately under the Accula brand name, though the volume of available tests was not disclosed.... Company's Press Release (March 24, 2020): https://www.mesabiotech.com/news/euacoronavirus FDA Approval Letter (March 23, 2020): https://www.fda.gov/media/136345/download
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Juan Lama
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In the high-stakes world of coronavirus testing, false positives are widely considered to be benign in comparison with false negatives, which can deprive infected people of treatment and embolden them to mingle with others, hastening the spread of disease. But false positives, which incorrectly identify a healthy person as infected by the virus, can have serious consequences as well, especially in places where the virus is scarce. False positives are generally very rare among tests that have been vetted by the Food and Drug Administration. But any test can be plagued by contamination, mishandling or technical glitches, leading a device to spot the coronavirus where it is not. In places where the virus is relatively scarce, false positives may even outnumber accurate positives — eroding trust in tests and, under some circumstances, prompting outbreaks of their own. Adverse effects include: -
Unnecessary isolation: According to guidelines published by the Centers for Disease Control and Prevention, people who test positive should immediately isolate themselves for at least 10 days after their symptoms start (if they experience symptoms at all). That’s 10 days spent away from friends and family, and 10 days of potential productivity in a school or workplace lost. -
New outbreaks: Under certain circumstances, a false positive could seed new coronavirus cases. Crowded facilities, such as nursing homes, prisons or hospitals, might isolate coronavirus-positive people together. “If someone isn’t actually positive, we could be sending them to their death,” said Dr. Valerie Fitzhugh, a pathologist at Rutgers University in New Jersey. -
Missed or inappropriate treatment: People with the flu or Covid-19 often show similar symptoms, but may be tested for only one of them at a time. If a patient is given an incorrect diagnosis of Covid-19, that person could be deprived of treatment that could alleviate their illness, or be given a costly therapy that does little to speed their recovery. -
A false sense of security: Mounting evidence suggests that most people who have fought off the coronavirus retain a degree of immunity. Scientists don’t know how long this immunity lasts, but C.D.C. guidelines note that reinfection is unlikely within 90 days. People who don’t have symptoms within this time window do not need to be tested again, the agency has said. Should someone be dropped from routine testing, said Dr. Catherine O’Neal, an infectious disease specialist at Louisiana State University, it would imperil that person’s health and could put an entire group of close contacts at risk
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Juan Lama
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The most widely used diagnostic test for the virus, called a PCR test, provides a simple yes-no answer to the question of whether a patient is infected. But the results sent to doctors and patients do not include something else the tests reveal: an indication of the amount of virus in the patient’s body, which is a signal of how contagious the person may be. That means many more people than necessary are being required to isolate and submit to contact tracing, and that the true picture of the state of the virus is skewed, according to reporting by Apoorva Mandavilli of The Times. The findings suggest that shifting to faster, less sensitive tests may help communities get a better handle on the virus. “We’ve been using one type of data for everything, and that is just plus or minus — that’s all,” said Dr. Michael Mina, an epidemiologist at the Harvard T.H. Chan School of Public Health. “We’re using that for clinical diagnostics, for public health, for policy decision-making.” The PCR test amplifies genetic matter from the virus in cycles. Large viral loads take fewer cycles to register, while even small amounts of virus — or inactive virus fragments — will register if enough cycles are run. (Dr. Mina thinks the cutoff in cycles should be no more than 30, to limit positives for samples with very little virus.) The number of cycles at which the virus registers is called the cycle threshold, or C.T. The Centers for Disease Control and Prevention said that it was examining the use of C.T. measures “for policy decisions,” and that it would need to collaborate with the Food and Drug Administration and device manufacturers to ensure the measures “can be used properly and with assurance that we know what they mean.” In three sets of testing data that did include C.T. values, compiled by officials in Massachusetts, New York and Nevada, up to 90 percent of positive samples barely carried any virus, a review by The Times found. If that rate applied nationwide, then only about 4,500 of the 45,604 new U.S. cases reported on Thursday would actually require isolation and contact tracing. “It’s just kind of mind-blowing to me that people are not recording the C.T. values from all these tests — that they’re just returning a positive or a negative,” said Angela Rasmussen, a virologist at Columbia University in New York.
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Juan Lama
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Early and accurate detection is critical for preventing the spread of COVID-19 and providing appropriate care for patients. Nasopharyngeal (NP) swabs, which require inserting a long shaft into the nasal cavity to collect a sample from the back of the nose and throat, are currently the gold standard for collecting a specimen for diagnosis. But the procedure is technically challenging, often uncomfortable for patients and requires personal protective equipment that may be in short supply. Other approaches to collecting specimens—including from an oropharyngeal swab and sputum—have been tested in small studies, but there is uncertainty about which method is best for detecting the virus. In a new study published in EBioMedicine, investigators from Brigham and Women's Hospital conducted a systematic review and meta-analysis, analyzing data from more than 3,000 specimens to compare the three approaches. The team found that sputum testing detected the RNA of the virus that causes COVID-19 at significantly higher rates while oropharyngeal swab testing had lower rates. Regardless of the collection method, the earlier samples were collected after symptoms began, the higher the detection rate. "The accurate diagnosis of COVID-19 has implications for health care, return-to-work, infection control and public health," said corresponding author Jonathan Li, MD, a faculty member in the Division of Infectious Diseases at the Brigham. "Our gold standard in and out of the hospital is the nasopharyngeal swab, but there's a lot of confusion about which sampling modality is best and most sensitive. Our study shows that sputum testing resulted in significantly higher rates of SARS-CoV-2 detection and supports the use of this type of testing as a valuable method for the diagnosis and monitoring of COVID-19 patients." Li and his colleagues scoured the literature—both preprints and published papers—for studies that assessed at least two respiratory sampling sites using an NP swab, oropharyngeal swab or sputum. From more than 1,000 studies, they identified 11 that met their criteria. These studies included results from a total of 3,442 respiratory tract specimens. The team examined how often each collection method produced a positive result. For NP swabs, the rate was 54 percent; for oropharyngeal swabs, 43 percent; for sputum, 71 percent. The rate of viral detection was significantly higher in sputum than either oropharyngeal swabs or NP swabs. Detection rates were highest within one week of symptom onset for all three tests. Study Published in EbioMedicine (July 18, 2020): https://doi.org/10.1016/j.ebiom.2020.102903
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Juan Lama
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Testing for the novel coronavirus in the Seattle area will get a huge boost in the coming weeks as a project funded by Bill Gates and his foundation begins offering home-testing kits that will allow people who fearthey may be infected to swab their noses and send the samples back for analysis. Results, which should be available in one to two days, will be shared with local health officials who will notify those who test positive. Via online forms, infected people can answer questions about their movements and contacts, making it easier for health officials to locate others who may need to be tested or quarantined, as well as to track the virus’ spread and identify possible hot spots. The goal is to eventually be able to process thousands of tests a day, said Scott Dowell, leader of coronavirus response at the Bill & Melinda Gates Foundation. The project is ramping up as quickly as possible, but it’s not clear exactly when it will launch, he added. Among other things, software needs to be upgraded to handle the expected crush of requests, and a detailed questionnaire finalized for people who request tests. “Although there’s a lot to be worked out, this has enormous potential to turn the tide of the epidemic,” Dowell said. While Public Health – Seattle & King County has confirmed 71 cases and 15 deaths as of Saturday, modeling by Trevor Bedford, a computational biologist at Fred Hutchinson Cancer Research Center, estimated on Wednesday that the actual number of cases in the Seattle area was about 600. Unchecked, that could theoretically increase to 12,000 cases – and possibly as many as 30,000 – by the end of March, according to projections from Mike Famulare at the Institute for Disease Modeling in Bellevue. But steps to slow transmission can significantly reduce the number of new infections, underscoring the importance of acting quickly to protect people from the virus. The new effort aims to leverage the formidable resources and expertise of the Gates Foundation, known for fighting disease and epidemics around the globe, to assist local health agencies struggling to keep up with a fast-moving outbreak.....
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